EP2028187A1 - Human and mouse targeting peptides identified by phage display - Google Patents

Human and mouse targeting peptides identified by phage display Download PDF

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Publication number
EP2028187A1
EP2028187A1 EP08016646A EP08016646A EP2028187A1 EP 2028187 A1 EP2028187 A1 EP 2028187A1 EP 08016646 A EP08016646 A EP 08016646A EP 08016646 A EP08016646 A EP 08016646A EP 2028187 A1 EP2028187 A1 EP 2028187A1
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seq
peptide
phage
peptides
cell
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French (fr)
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Wadih Arap
Renata Pasqualini
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University of Texas System
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University of Texas System
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P13/00—Drugs for disorders of the urinary system
    • A61P13/02—Drugs for disorders of the urinary system of urine or of the urinary tract, e.g. urine acidifiers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
    • A61P15/18—Feminine contraceptives
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A61P3/04—Anorexiants; Antiobesity agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
    • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
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    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A—HUMAN NECESSITIES
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    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P9/00—Drugs for disorders of the cardiovascular system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P9/00—Drugs for disorders of the cardiovascular system
    • A61P9/10—Drugs for disorders of the cardiovascular system for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1037—Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/525—Virus
    • A61K2039/5256—Virus expressing foreign proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2810/00—Vectors comprising a targeting moiety
    • C12N2810/40—Vectors comprising a peptide as targeting moiety, e.g. a synthetic peptide, from undefined source
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention concerns the fields of molecular medicine and targeted delivery of therapeutic agents. More specifically, the present invention relates to compositions and methods for identification and use of peptides that selectively target organs tissues or cell types in vivo or in vitro.
  • Therapeutic treatment of many disease states is limited by the systemic toxicity of the therapeutic agents used. Cancer therapeutic agents in particular exhibit a very low therapeutic index, with rapidly growing normal tissues such as skin and bone marrow affected at concentrations of agent that are not much higher than the concentrations used to kill tumor cells. Treatment of cancer and other organ, tissue or cell type confined disease states would be greatly facilitated by the development of compositions and methods for targeted delivery to a desired organ, tissue or cell type of a therapeutic agent.
  • Phage display libraries expressing transgenic peptides on the surface of bacteriophage were initially developed to map epitope binding sites of immunoglobulins (Smith and Scott, 1986, 1993). Such libraries can be generated by inserting random oligonucleotides into cDNAs encoding a phage surface protein, generating collections of phage particles displaying unique peptides in as many as 10 9 permutations. (Pasqualini and Ruoslahti, 1996, Arap et al, 1998a; Arap et al 1998b).
  • Attachment of therapeutic agents to targeting peptides resulted in the selective delivery of the agent to a desired organ, tissue or cell type in the mouse model system.
  • Targeted delivery of chemotherapeutic agents and proapoptotic peptides to receptors located in tumor angiogenic vasculature resulted in a marked increase in therapeutic efficacy and a decrease in systemic toxicity in tumor-bearing mouse models (Arap et al., 1998a, 1998b; Ellerby et al., 1999).
  • the present invention solves a long-standing need in the art by providing compositions and methods for the identifying and using targeting peptides that are selective for organs, tissues or specific cell types.
  • the methods concern Biopanning and Rapid Analysis of Selective Interactive Ligands (BRASIL), a novel method for phage display that results in decreased background of non-specific phage binding, while retaining selective binding of phage to cell receptors.
  • BRASIL Biopanning and Rapid Analysis of Selective Interactive Ligands
  • targeting peptides are identified by exposing a subject to a phage display library, collecting samples of one or more organs, tissues or cell types, separating the samples into isolated cells or small clumps of cells suspended in an aqueous phase, layering the aqueous phase over an organic phase, centrifuging the two phases so that the cells are pelleted at the bottom of a centrifuge tube and collecting phage from the pellet.
  • the organic phase is dibutylphtalate.
  • phage that bind to a target organ, tissue or cell type may be pre-screened or post-screened against a subject lacking that organ, tissue or cell type. Phage that bind to the subject lacking the target organ, tissue or cell type are removed from the library prior to screening in subjects possessing the organ, tissue or cell type.
  • the organ, tissue or cell type is placenta or adipose tissue.
  • targeting phage may be recovered from specific cell types or sub-types present in an organ or tissue after selection of the cell type by PALM (Positioning and Ablation with Laser Microbeams).
  • PALM allows specific cell types to be selected from, for example, a thin section of an organ or tissue. Phage may be recovered from the selected sample.
  • a phage display library displaying the antigen binding portions of antibodies from a subject is prepared, the library is screened against one or more antigens and phage that bind to the antigens are collected.
  • the antigen is a targeting peptide.
  • the methods and compositions may be used to identify one or more receptors for a targeting peptide.
  • the compositions and methods may be used to identify naturally occurring ligands for known or newly identified receptors.
  • the methods may comprise contacting a targeting peptide to an organ, tissue or cell containing a receptor of interest, allowing the peptide to bind to the receptor, and identifying the receptor by its binding to the peptide.
  • the targeting peptide contains at least three contiguous amino acids selected from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID NO:251.
  • the targeting peptide comprises a portion of an antibody against the receptor.
  • the targeting peptide may contain a random amino acid sequence.
  • the contacting step can utilize intact organs, tissues or cells, or may alternatively utilize homogenates or detergent extracts of the organs, tissues or cells.
  • the cells to be contacted may be genetically engineered to express a suspected receptor for the targeting peptide.
  • the targeting peptide is modified with a reactive moiety that allows its covalent attachment to the receptor.
  • the reactive moiety is a photoreactive group that becomes covalently attached to the receptor when activated by light.
  • the peptide is attached to a solid support and the receptor is purified by affinity chromatography.
  • the solid support comprises magnetic beads, Sepharose beads, agarose beads, a nitrocellulose membrane, a nylon membrane, a column chromatography matrix, a high performance liquid chromatography (HPLC) matrix or a fast performance liquid chromatography (FPLC) matrix.
  • the targeting peptide inhibits the activity of the receptor upon binding to the receptor.
  • receptor activity can be assayed by a variety of methods known in the art, including but not limited to catalytic activity and binding activity.
  • the receptor is an endostatin receptor, a metalloprotease or an aminopeptidase.
  • one or more ligands for a receptor of interest may be identified by the disclosed methods and compositions.
  • One or more targeting peptides that mimic part or all of a naturally occurring ligand may be identified by phage display and biopanning in vivo or in vitro .
  • a naturally occurring ligand may be identified by homology with a single targeting peptide that binds to the receptor, or a consensus motif of sequences that bind to the receptor.
  • an antibody may be prepared against one or more targeting peptides that bind to a receptor of interest. Such antibodies may be used for identification or immunoaffinity purification of the native ligand.
  • the targeting peptides of the present invention are of use for the selective delivery of therapeutic agents, including but not limited to gene therapy vectors and fusion proteins, to specific organs, tissues or cell types.
  • therapeutic agents including but not limited to gene therapy vectors and fusion proteins
  • the skilled artisan will realize that the scope of the claimed methods of use include any disease state that can be treated by targeted delivery of a therapeutic agent to a desired organ, tissue or cell type.
  • disease states include those where the diseased cells are confined to a specific organ, tissue or cell type, such as non-metastatic cancer, other disease states may be treated by an organ, tissue or cell type-targeting approach.
  • One embodiment of the present invention concerns isolated peptides of 100 amino acids or less in size, comprising at least 3 contiguous amino acids of a targeting peptide sequence, selected from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID NO:251.
  • the isolated peptide is 50 amino acids or less, more preferably 30 amino acids or less, more preferably 20 amino acids or less, more preferably 10 amino acids or less, or even more preferably 5 amino acids or less in size.
  • the isolated peptide of claim 1 comprises at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 contiguous amino acids of a targeting peptide sequence, selected from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID NO:251.
  • the isolated peptide is attached to a molecule.
  • the attachment is a covalent attachment.
  • the molecule is a drug, a chemotherapeutic agent, a radioisotope, a pro-apoptosis agent, an anti-angiogenic agent, a hormone, a cytokine, a growth factor, a cytotoxic agent, a peptide, a protein, an antibiotic, an antibody, a Fab fragment of an antibody, a survival factor, an anti-apoptotic factor, a hormone antagonist, an imaging agent, a nucleic acid or an antigen.
  • Those molecules are representative only.
  • Molecules within the scope of the present invention include virtually any molecule that may be attached to a targeting peptide and administered to a subject.
  • the pro-aptoptosis agent is gramicidin, magainin, mellitin, defensin, cecropin, (KLAKLAK) 2 (SEQ ID NO:1), (KLAKKLA) 2 (SEQ ID NO:2), (KAAKKAA) 2 (SEQ ID NO:3) or (KLGKKLG) 3 (SEQ ID NO:4).
  • the anti-angiogenic agent is angiostatin5, pigment epithelium-drived factor, angiotensin, laminin peptides, fibronectin peptides, plasminogen activator inhibitors, tissue metalloproteinase inhibitors, interferons, interleukin 12, platelet factor 4, IP-10, Gro-B, thrombospondin, 2-methoxyoestradiol, proliferin-related protein, carboxiamidotriazole, CM101, Marimastat, pentosan polysulphate, angiopoietin 2 (Regeneron), interferon-alpha, herbimycin A, PNU145156E, 16K prolactin fragment, Linomide, thalidomide, pentoxifylline, genistein, TNP-470, endostatin, paclitaxel, docetaxel, polyamines, a proteasome inhibitor, a kinase inhibitor, a signaling inhibitor (
  • the cytokine is interleukin 1 (IL-1), IL-2, IL-5, IL-10, JL-11, IL-12, IL-18, interferon- ⁇ (IF- ⁇ ), IF- ⁇ , IF-B, tumor necrosis factor- ⁇ (TNF- ⁇ ), or GM-CSF (granulocyte macrophage colony stimulating factor).
  • IL-1 interleukin 1
  • IL-2 interleukin-2
  • IL-5 interferon- ⁇
  • IF- ⁇ IF- ⁇
  • IF-B tumor necrosis factor- ⁇
  • TNF- ⁇ tumor necrosis factor- ⁇
  • GM-CSF granulocyte macrophage colony stimulating factor
  • the isolated peptide is attached to a macromolecular complex.
  • the attachment is a covalent attachment.
  • the macromolecular complex is a virus, a bacteriophage, a bacterium, a liposome, a microparticle, a magnetic bead, a yeast cell, a mammalian cell, a cell or a microdevice. These are representative examples only. Macromolecular complexes within the scope of the present invention include virtually any macromolecular complex that may be attached to a targeting peptide and administered to a subject.
  • the isolated peptide is attached to a eukaryotic expression vector, more preferably a gene therapy vector.
  • the isolated peptide is attached to a solid support, preferably magnetic beads, Sepharose beads, agarose beads, a nitrocellulose membrane, a nylon membrane, a column chromatography matrix, a high performance liquid chromatography (HPLC) matrix or a fast performance liquid chromatography (FPLC) matrix.
  • a solid support preferably magnetic beads, Sepharose beads, agarose beads, a nitrocellulose membrane, a nylon membrane, a column chromatography matrix, a high performance liquid chromatography (HPLC) matrix or a fast performance liquid chromatography (FPLC) matrix.
  • Additional embodiments of the present invention concern fusion proteins comprising at least 3 contiguous amino acids of a sequence selected from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID N0:251.
  • compositions comprising the claimed isolated peptides or fusion proteins in a pharmaceutically acceptable carrier.
  • kits comprising the claimed isolated peptides or fusion proteins in one or more containers.
  • a targeting peptide for a desired organ, tissue or cell type attaching said targeting peptide to a molecule, macromolecular complex or gene therapy vector, and providing said peptide attached to said molecule, complex or vector to a subject.
  • the targeting peptide is selected to include at least 3 contiguous amino acids from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID NO:251.
  • the organ, tissue or cell type is bone marrow, lymph node, prostate cancer or prostate cancer that has metastasized to bone marrow.
  • the molecule attached to the targeting peptide is a chemotherapeutic agent, an antigen or an imaging agent.
  • chemotherapeutic agent an antigen or an imaging agent.
  • any organ, tissue or cell type can be targeted for delivery, using targeting peptides attached to any molecule, macromolecular complex or gene therapy vector.
  • nucleic acids of 300 nucleotides or less in size encoding a targeting peptide.
  • the isolated nucleic acid is 250, 225, 200, 175, 150, 125, 100, 75, 50, 40, 30, 20 or even 10 nucleotides or less in size.
  • the isolated nucleic acid is incorporated into a eukaryotic or a prokaryotic expression vector.
  • the vector is a plasmid, a cosmid, a yeast artificial chromosome (YAC), a bacterial artificial chromosome (BAC), a virus or a bacteriophage.
  • the isolated nucleic acid is operatively linked to a leader sequence that localizes the expressed peptide to the extracellular surface of a host cell.
  • Additional embodiments of the present invention concern methods of treating a disease state comprising selecting a targeting peptide that targets cells associated with the disease state, attaching one or more molecules effective to treat the disease state to the peptide, and administering the peptide to a subject with the disease state.
  • the targeting peptide includes at least three contiguous amino acids selected from any of SEQ ID NO:5 through SEQ ID NO:45, SEQ ID NO:47 through SEQ ID NO:121, SEQ ID NO:123 and SEQ ID NO:125 through SEQ ID NO:251.
  • the disease state is diabetes mellitus, inflammatory disease, arthritis, atherosclerosis, cancer, autoimmune disease, bacterial infection, viral infection, cardiovascular disease or degenerative disease.
  • Tumor targeting peptides identified by the methods disclosed in the instant application may be attached to therapeutic agents, including but not limited to molecules or macromolecular assemblages and administered to a subject with cancer, providing for increased efficacy and decreased systemic toxicity of the therapeutic agent.
  • therapeutic agents within the scope of the present invention include but are not limited to chemotherapeutic agents, radioisotopes, pro-apoptosis agents, cytotoxic agents, cytostatic agents and gene therapy vectors.
  • tumor targeting peptide is incorporated into the capsule of a phage gene therapy vector to target delivery of the phage to angiogenic endothelial cells in tumor blood vessels.
  • the antigen comprises one or more targeting peptides.
  • the targeting peptides are prepared and immobilized on a solid support, serum containing antibodies is added and antibodies that bind to the targeting peptides are collected.
  • FIG.1 Validation of placenta homing phage.
  • Phage bearing targeting peptides identified in Example 3 were injected into pregnant mice and their recovery from placenta was compared to control fd-tet phage without targeting sequences.
  • the placenta homing phage clones were: PA - TPKTSVT (SEQ ID NO:39), PC - RAPGGVR (SEQ ID NO:41), PE - LGLRSVG (SEQ ID NO:44), PF - YIRPFTL (SEQ ID NO:43).
  • FIG. 2 Validation of adipose homing peptides. Phage bearing targeting peptides identified in Example 4 were injected into pregnant mice and their recovery from adipose tissue was compared to control fd-tet phage without targeting sequences.
  • FIG. 3 Spleen targeting in vitro using BRASIL. Binding of Fab clones #2, #6, #10, #12 and control Fab clone NPC-3TT was compared to binding of control Fd-tet phage.
  • FIG. 4 Spleen targeting in vitro using BRASIL. Binding of Fab clones #2, #6, #10, #12 and control Fab clone NPC-3TT were directly compared to each other.
  • FIG. 5 Spleen targeting in vivo using BASIL. Binding of Fab clones #2, #6, #10, #12 was compared to binding of Fd-tet phage.
  • FIG. 6 Spleen targeting in vivo using BRASIL. Binding of Fab clone #10 to spleen tissue was compared to binding of Fab control clone NPC-3TT and Fd-tet phage.
  • FIG. 7 Binding of Fab clone #10 to spleen versus bone marrow in comparison to Fd-tet phage.
  • FIG. 8 Binding of Fab clones from an anti-Karposi's sarcoma library to angiogenic retina.
  • FIG. 9 Binding of B3 cytoplasmic domain-selected phage to immobilized proteins.
  • GST fusion proteins or GST alone were coated on microtiter wells at 10 ⁇ g/ml and used to bind phage expressing endostatin targeting peptides.
  • Each phage is identified by the peptide sequence it displayed: GLDTYRGSP (SEQ ID NO:96); YDWWYPWSW (SEQ ID NO:95); CLRQSYSYIVC (SEQ ID NO:104); SDNRYIGSW (SEQ ID NO:97); CEQRQTQEGC (SEQ ID NO:93); CFQNRC (SEQ ID NO:102).
  • the data represent the mean colony counts from triplicate wells, with standard error of less than 10% of the mean.
  • FIG. 10 Binding of ⁇ 5 cytoplasmic domain-selected phage to immobilized proteins.
  • GST fusion proteins or GST alone were coated on microtiter wells at 10 ⁇ g/ml and used to bind phage expressing endostatin binding peptides.
  • Each phage is identified by the peptide sequence it displayed: (A) DEEGYYMMR (SEQ ID NO:110); (B) KQFSYRYLL (SEQ ID NO:111); (C) CEPYWDGWFC (SEQ ID NO:106); (D) VVISYSMPD (SEQ ID NO:112); and (E) CYIWPDSGLC (SEQ ID NO:105).
  • the data represent the mean colony counts from triplicate wells, with standard error less than 10% of the mean.
  • FIG. 11 Binding of the cytoplasmic-domain binding phage to ⁇ 3 immobilized protein and inhibition with the synthetic peptide. Phage were incubated on wells coated with GST- ⁇ 3cyto in the presence of increasing concentrations of the corresponding synthetic peptide or a control peptide. The data represent the mean colony counts from triplicate wells, with standard error less than 10% of the mean.
  • FIG. 12 Binding of the cytoplasmic-domain binding phage to ⁇ 5 immobilized protein and inhibition with the synthetic peptide. Phage were incubated on wells coated with GST- ⁇ 5cyto in the presence of increasing concentrations of the corresponding synthetic peptide or a control peptide. The data represent the mean colony counts from triplicate wells, with standard error less than 10% of the mean.
  • FIG. 13 Binding of phage to immobilized ⁇ 3-GST and ⁇ 5-GST after phosphorylation. Phage were phosphorylated with Fyn kinase. Insertless phage were used as a control. Phage were incubated on wells coated with GST- ⁇ 3cyto or GST- ⁇ 3cyto. The data represent the mean colony counts from triplicate wells, with standard error less than 10% of the mean.
  • FIG. 14 Binding of phage to immobilized GST fusion proteins after phosphorylation. Phages were phosphorylated with Fyn kinase. Insertless phage was used as a control. Phage were incubated on wells coated with GST-cytoplasmic domains. The data represent the mean of colony counts from triplicate wells, with standard error less than 10% of the mean.
  • FIG. 15 Effect of integrin cytoplasmic domain binding peptides on cell proliferation. Serum-deprived cells were cultured for 24 h.and the proliferation was determined by [ 3 H] thymidine (1 ⁇ Ci/ml) uptake measurements. In a positive control, VEGF was added back to serum-starved cells. Each experiment was performed three times with triplicates, and the results were expressed as the mean +/- SD.
  • FIG. 16 Effect of penetratin peptide chimeras on endothelial cell migration.
  • Cell migration assay were performed in a 48-well microchemotaxis chamber. Five random high-power fields (magnitude 40 ⁇ ) were counted in each well. The results show that both ⁇ 3-integrin cytoplasmic domain binding peptides (Y-18 and TYR-11) increase cell migration while penetratin does not affect the cells.
  • FIG. 17 Penetratin peptide chimera binding to the ⁇ 5 cytoplasmic domain induces programmed cell death.
  • 10 6 HUVEC cells were harvested in complete media and 15 ⁇ M penetratin peptide chimeras were added to the cells. After four, eight and twelve hours the cells were stained with Propidium Iodide (PI) and induction of apoptosis was analyzed by cytometric analysis.
  • PI Propidium Iodide
  • FIG. 18 Specificity of the antibodies raised against B3- or ⁇ 5-selected phage (ELISA). Increasing dilutions of sera obtained after three immunizations with GLDTYRGSP (SEQ ID NO:96) or SDNRYIGSW (SEQ ID NO:97) conjugated to KLH were incubated on microtiterwells coated with 10 ⁇ g of SDNRYIGSW (SEQ ID NO:97, Y-18), GLDTYRGSP (SEQ ID NO:96, TYR-11) or control peptides. Preimmunesera were used as controls. After incubation with HRPgoat anti-rabbit, OD was measured at 405 nm. The data represent the means from triplicate wells, with standard error less than 10%.
  • FIG. 19 Specificity of the antibodies raised against ⁇ 3- or ⁇ 5-selected phage (ELISA).
  • Sera obtained after three immunizations with SDNRYIGSW (SEQ ID NO:97, Y-18) or GLDTYRGSP (SEQ ID NO:96, TYR-11) conjugated to KLH were incubated in microtiter wells coated with 10 ⁇ g of TYR-11 or Y-18.
  • GLDTYRGSP (SEQ ID NO:96) or SDNRYIGSW (SEQ ID NO:97) and control peptides were added in solution. After incubation with HRP goat anti-rabbit, OD was measured at 405 nm. The data represent the means from triplicate wells, with standard error less than 10%. Peptides added in solution specifically block the reactivity with the immobilized peptides.
  • FIG. 20A Competitive binding of Annexin V to ⁇ 5 integrin with VISY peptide. Binding assays were performed by ELISA.
  • FIG. 20B Relative levels of binding of anti-Annexin V antibody to purified Annexin V protein and VISY peptide.
  • FIG. 21 Chimeric peptide containing VISY peptide linked to penetratin (antennapedia) induces apoptosis. VISY induced apoptosis was inhibited by addition of a caspase inhibitor (zVAD).
  • zVAD caspase inhibitor
  • FIG. 22 APA-binding phage specifically bind tumors. Equal amounts of phage were injected into the tail veins of mice bearing MDA-MB-435-derived tumors and phage were recovered after perfusion. Mean values for phage recovered from the tumor or control tissue (brain) and the standard error from triplicate platings are shown.
  • FIG. 23 CPRECESIC (SEQ ID NO:123) is a specific inhibitor of APA activity. APA enzyme activity was assayed in the presence of increasing concentrations of either GACVRLSACGA (SEQ ID NO:124) (control) or CPRECESIC (SEQ ID NO:123) peptide. The IC 50 for APA inhibition by CPRECESIC (SEQ ID NO:123) was estimated at 800 ⁇ M. Error bars are the standard error of the means of triplicate wells. The experiment was repeated three times with similar results.
  • FIG. 24 CPRECESIC (SEQ ID NO:123) inhibits HUVEC migration.
  • HUVECs were stimulated with VEGF-A (10 ng/ml). The assay was performed in a Boyden microchemotaxis chamber, and cells were allowed to migrate through an 8- ⁇ m pore filter for 5 h at 37°C.
  • GACVRLSACGA SEQ ID NO:124
  • CPRECESIC SEQ ID NO:123
  • Migrated cells were stained and five high-power fields (magnitude 100x) for each microwell were counted. Error bars are the standard error of the means of triplicate microwells.
  • FIG. 25 CPRECESIC (SEQ ID NO:123) inhibits HUVEC proliferation.
  • Cells were stimulated with VEGF-A (10 ng/ml), and growth was evaluated at the indicated times by a colorimetric assay based on crystal violet staining. Error bars are the standard error of the means of triplicate wells. Each experiment was repeated at least twice with similar results.
  • FIG. 26 Protocol for in vivo biopanning for phage targeted in mouse pancreas, kidneys, liver, lungs and adrenal gland.
  • FIG. 27 Protocol for recovery of phage by infection of E . coli or recovery of phage DNA by amplification and subcloning.
  • FIG. 28 Pancreatic islet targeting peptides and homologous proteins.
  • FIG. 29 Pancreatic islet targeting peptides and homologous proteins.
  • FIG. 30 Pancreatic islet targeting peptides and homologous proteins.
  • FIG. 31 Pancreatic islet targeting peptides and homologous proteins.
  • a or “an” may mean one or more.
  • the words “a” or “an” may mean one or more than one.
  • another may mean at least a second or more of an item.
  • a “targeting peptide” is a peptide comprising a contiguous sequence of amino acids, that is characterized by selective localization to an organ, tissue or cell type. Selective localization may be determined, for example, by methods disclosed below, wherein the putative targeting peptide sequence is incorporated into a protein that is displayed on the outer surface of a phage. Administration to a subject of a library of such phage that have been genetically engineered to express a multitude of such targeting peptides of different amino acid sequence is followed collection of one or more organs, tissues or cell types from the subject and identification of phage found in that organ, tissue or cell type.
  • a phage expressing a targeting peptide sequence is considered to be selectively locallized to a tissue or organ if it exhibits greater binding in that tissue or organ compared to a control tissue or organ.
  • selective localization of a targeting peptide should result in a two-fold or higher enrichment of the phage in the target organ, tissue or cell type, compared to a control organ, tissue or cell type.
  • Selective localization resulting in at least a three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, ten-fold or higher enrichment in the target organ compared to a control organ, tissue or cell type is more preferred.
  • a phage expressing a targeting peptide sequence that exhibits selective localization preferably shows an increased enrichment in the target organ compared to a control organ when phage recovered from the target organ are reinjected into a second host for another round of screening. Further enrichment may be exhibited following a third round of screening.
  • Another alternative means to determine selective localization is that phage expressing the putative target peptide preferably exhibit a two-fold, more preferably a three-fold or higher enrichment in the target organ compared to control phage that express a non-specific peptide or that have not been genetically engineered to express any putative target peptides.
  • Targeting peptide and “homing peptide” are used synonymously herein.
  • a "phage display library” means a collection of phage that have been genetically engineered to express a set of putative targeting peptides on their outer surface.
  • DNA sequences encoding the putative targeting peptides are inserted in frame into a gene encoding a phage capsule protein.
  • the putative targeting peptide sequences are in part random mixtures of all twenty amino acids and in part non-random.
  • the putative targeting peptides of the phage display library exhibit one or more cysteine residues at fixed locations within the targeting peptide sequence.
  • a "macromolecular complex” refers to a collection of molecules that may be random, ordered or partially ordered in their arrangement.
  • the term encompasses biological organisms such as bacteriophage, viruses, bacteria, unicellular pathogenic organisms, multicellular pathogenic organisms and prokaryotic or eukaryotic cells.
  • the term also encompasses non-living assemblages of molecules, such as liposomes, microcapsules, microparticles, magnetic beads and microdevices. The only requirement is that the complex contains more than one molecule.
  • the molecules may be identical, or may differ from each other.
  • a "receptor" for a targeting peptide includes but is not limited to any molecule or complex of molecules that binds to a targeting peptide.
  • Non-limiting examples of receptors include peptides, proteins, glycoproteins, lipoproteins, epitopes, lipids, carbohydrates, multi-molecular structures, a specific conformation of one or more molecules and a morphoanatomic entity.
  • a "receptor” is a naturally occurring molecule or complex of molecules that is present on the lumenal surface of cells forming blood vessels within a target organ, tissue or cell type.
  • a “subject” refers generally to a mammal. In certain preferred embodiments, the subject is a mouse or rabbit. In even more preferred embodiments, the subject is a human.
  • the methods described herein for identification of targeting peptides involve the in vivo administration of phage display libraries.
  • Various methods of phage display and methods for producing diverse populations of peptides are well known in the art.
  • U.S. Pat. Nos. 5,223,409 ; 5,622,699 and 6,068,829 each of which is incorporated herein by reference, disclose methods for preparing a phage library.
  • the phage display technique involves genetically manipulating bacteriophage so that small peptides can be expressed on their surface (Smith et al, 1985, 1993).
  • peptide libraries have made it possible to characterize interacting sites and receptor-ligand binding motifs within many proteins, such as antibodies involved in inflammatory reactions or integrins that mediate cellular adherence.
  • This method has also been used to identify novel peptide ligands that serve as leads to the development of peptidomimetic drugs or imaging agents (Arap et al ., 1998a).
  • larger protein domains such as single-chain antibodies can also be displayed on the surface of phage particles (Arap et al., 1998a).
  • Targeting amino acid sequences selective for a given organ, tissue or cell type can be isolated by "biopanning" (Pasqualini and Ruoslahti, 1996; Pasqualini, 1999).
  • biopanning a library of phage containing putative targeting peptides is administered to an animal or human and samples of organs, tissues or cell types containing phage are collected.
  • the phage may be propagated in vitro between rounds of biopanning in pilus-positive bacteria. The bacteria are not lysed by the phage but rather secrete multiple copies of phage that display a particular insert.
  • Phage that bind to a target molecule can be eluted from the target organ, tissue or cell type and then amplified by growing them in host bacteria. If desired, the amplified phage can be administered to a host and samples of organs, tissues or cell types again collected. Multiple rounds of biopanning can be performed until a population of selective binders is obtained.
  • the amino acid sequence of the peptides is determined by sequencing the DNA corresponding to the targeting peptide insert in the phage genome. The identified targeting peptide can then be produced as a synthetic peptide by standard protein chemistry techniques (Arap et al ., 1998a, Smith et al ., 1985).
  • a candidate target is identified as the receptor of a targeting peptide, it can be isolated, purified and cloned by using standard biochemical methods (Pasqualini, 1999; Rajotte and Ruoslahti, 1999).
  • a subtraction protocol is used with to further reduce background phage binding.
  • the purpose of subtraction is to remove phage from the library that bind to cells other than the cell of interest, or that bind to inactivated cells.
  • the phage library may be prescreened against a subject who does not possess the targeted cell, tissue or organ. For example, placenta binding peptides may be identified after prescreening a library against a male or non-pregnant female subject After subtraction the library may be screened against the cell, tissue or organ of interest.
  • an unstimulated, quiescent cell type, tissue or organ may be screened against the library and binding phage removed.
  • the cell line, tissue or organ is then activated, for example by administration of a hormone, growth factor, cytokine or chemokine and the activated cell type, tissue or organ screened against the subtracted phage library.
  • Phage libraries displaying linear, cyclic, or double cyclic peptides may be used within the scope of the present invention. However, phage libraries displaying 3 to 10 random residues in a cyclic insert (CX 3-10 C) are preferred, since single cyclic peptides tend to have a higher affinity for the target organ than linear peptides. Libraries displaying double-cyclic peptides (such as CX 3 C X 3 CX 3 C; Rojotte et al., 1998) have been successfully used. However, the production of the cognate synthetic peptides, although possible, can be complex due to the multiple conformers with different dissulfide bridge arrangements.
  • a means of identifying peptides that home to the angiogenic vasculature of tumors has been devised, as described below.
  • a panel of peptide motifs that target the blood vessels of tumor xenografts in nude mice has been assembled (Arap et al., 1998a; reviewed in Pasqualini, 1999). These motifs include the sequences RGD-4C, NGR, and GSL.
  • the RGD-4C peptide has previously been identified as selectively binding ⁇ v integrins and has been shown to home to the vasculature of tumor xenografts in nude mice (Arap et al ., 1998a, 1998b; Pasqualini et al., 1997).
  • the receptors for the tumor homing RGD4C targeting peptide has been identified as ⁇ v integrins (Pasqualini et al., 1997).
  • the ⁇ v integrins play an important role in angiogenesis.
  • the ⁇ v ⁇ 3 and ⁇ v ⁇ 5 integrins are absent or expressed at low levels in normal endothelial cells but are induced in angiogenic vasculature of tumors (Brooks et al ., 1994; Hammes et al ., 1996).
  • Aminopeptidase N/CD13 has recently been identified as an angiogenic receptor for the NGR motif (Burg et al., 1999). Aminopeptidase N/CD13 is strongly expressed not only in the angiogenic blood vessels of prostate cancer in TRAMP mice but also in the normal epithelial prostate tissue.
  • Tumor-homing phage co-localize with their receptors in the angiogenic vasculature of tumors but not in non-angiogenic blood vessels in normal tissues (Arap et al ., 1998b). Immunohistochemical evidence shows that vascular targeting phage bind to human tumor blood vessels in tissue sections (Pasqualini et al., 2000) but not to normal blood vessels. A negative control phage with no insert (fd phage) did not bind to normal or tumor tissue sections. The expression of the angiogenic receptors was evaluated in cell lines, in non-proliferating blood vessels and in activated blood vessels of tumors and other angiogenic tissues such as corpus luteum.
  • Angiogenic neovasculature expresses markers that are either expressed at very low levels or not at all in non-proliferating endothelial cells (not shown).
  • the markers of angiogenic endothelium include receptors for vascular growth factors, such as specific subtypes of VEGF and basic FGF receptors, and ⁇ v integrins, among many others (Mustonen and Alitalo, 1995).
  • vascular growth factors such as specific subtypes of VEGF and basic FGF receptors, and ⁇ v integrins, among many others (Mustonen and Alitalo, 1995).
  • tumor vascular markers are proteases and some of the markers also serve as viral receptors.
  • Alpha v integrins are receptors for adenoviruses (Wickham et al ., 1997c) and CD13 is a receptor for coronaviruses (Look et al., 1989).
  • MMf-2 and MMP-9 are receptors for echoviruses (Koivunen et al ., 1999).
  • Aminopeptidase A also appears to be a viral receptor.
  • Bacteriophage may use the same cellular receptors as eukaryotic viruses.
  • separation of phage bound to the cells of a target organ, tissue or cell type from unbound phage is achieved using the BRASIL technique (Provisional Patent Application No. 60/231,266 filed September 8, 2000 ; U.S. Patent Application entitled, "Biopanning and Rapid Analysis of Selective Interactive Ligands (BRASIL)" by Arap, Pasqualini and Giordano, filed concurrently herewith, incorporated herein by reference in its entirety).
  • BRASIL Biopanning and Rapid Analysis of Soluble Interactive Ligands
  • an organ, tissue or cell type is gently separated into cells or small clumps of cells that are suspended in an aqueous phase.
  • the aqueous phase is layered over an organic phase of appropriate density and centrifuged.
  • BRASIL may be performed in an in vivo protocol, in which organs, tissues or cell types are exposed to a phage display library by intravenous administration, or by an ex vivo protocol, where the cells are exposed to the phage library in the aqueous phase before centrifugation.
  • the present invention concerns novel compositions comprising at least one protein or peptide.
  • a protein or peptide generally refers, but is not limited to, a protein of greater than about 200 amino acids, up to a full length sequence translated from a gene; a polypeptide of greater than about 100 amino acids; and/or a peptide of from about 3 to about 100 amino acids.
  • proteins proteins
  • polypeptide and “peptide are used interchangeably herein.
  • the size of the at least one protein or peptide may comprise, but is not limited to, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, about 110, about 120, aboout 130, about 140, about 150, about 160, about 170, about 180, about
  • amino acid residue refers to any naturally occuring amino acid, any amino acid derivitive or any amino acid mimic known in the art.
  • the residues of the protein or peptide are sequential, without any non-amino acid interrupting the sequence of amino acid residues.
  • the sequence may comprise one or more non-amino acid moieties.
  • the sequence of residues of the protein or peptide may be interrupted by one or more non-amino acid moieties.
  • protein or peptide encompasses amino acid sequences comprising at least one of the 20 common amino acids found in naturally occurring proteins, or at least one modified or unusual amino acid, including but not limited to those shown on Table 1 below. TABLE 1 Modified and Unusual Amino Acids Abbr. Amino Acid Abbr.
  • Proteins or peptides may be made by any technique known to those of skill in the art, including the expression of proteins, polypeptides or peptides through standard molecular biological techniques, the isolation of proteins or peptides from natural sources, or the chemical synthesis of proteins or peptides.
  • the nucleotide and protein, polypeptide and peptide sequences corresponding to various genes have been previously disclosed, and may be found at computerized databases known to those of ordinary skill in the art.
  • One such database is the National Center for Biotechnology Information's Genbank and GenPept databases (http://www.ncbi.nlm.nih.gov/) .
  • the coding regions for known genes may be amplified and/or expressed using the techniques disclosed herein or as would be know to those of ordinary skill in the art. Alternatively, various commercial preparations of proteins, polypeptides and peptides are known to those of skill in the art.
  • peptide mimetics are peptide-containing molecules that mimic elements of protein secondary structure. See, for example, Johnson et al., "Peptide Turn Mimetics” in BIOTECHNOLOGY AND PHARMACY, Pezzuto et al., Eds., Chapman and Hall, New York (1993 ), incorporated herein by reference.
  • the underlying rationale behind the use of peptide mimetics is that the peptide backbone of proteins exists chiefly to orient amino acid side chains in such a way as to facilitate molecular interactions, such as those of antibody and antigen.
  • a peptide mimetic is expected to permit molecular interactions similar to the natural molecule.
  • fusion proteins These molecules generally have all or a substantial portion of a targeting peptide, linked at the N- or C-terminus, to all or a portion of a second polypeptide or proteion.
  • fusions may employ leader sequences from other species to permit the recombinant expression of a protein in a heterologous host.
  • Another useful fusion includes the addition of an immunologically active domain, such as an antibody epitope, to facilitate purification of the fusion protein. Inclusion of a cleavage site at or near the fusion junction will facilitate removal of the extraneous polypeptide after purification.
  • fusion proteins include linking of functional domains, such as active sites from enzymes, glycosylation domains, cellular targeting signals or transmembrane regions.
  • the fusion proteins of the instant invention comprise a targeting peptide linked to a therapeutic protein or peptide.
  • proteins or peptides that may be incorporated into a fusion protein include cytostatic proteins, cytocidal proteins, pro-apoptosis agents, anti-angiogenic agents, hormones, cytokines, growth factors, peptide drugs, antibodies, Fab fragments antibodies, antigens, receptor proteins, enzymes, lectins, MHC proteins, cell adhesion proteins and binding proteins.
  • fusion protein comprising a targeting peptide.
  • Methods of generating fusion proteins are well known to those of skill in the art. Such proteins can be produced, for example, by chemical attachment using bifunctional cross-linking reagents, by de novo synthesis of the complete fusion protein, or by attachment of a DNA sequence encoding the targeting peptide to a DNA sequence encoding the second peptide or protein, followed by expression of the intact fusion protein.
  • a protein or peptide may be isolated or purified.
  • Protein purification techniques are well known to those of skill in the art. These techniques involve, at one level, the homogenization and crude fractionation of the cells, tissue or organ to polypeptide and non-polypeptide fractions.
  • the protein or polypeptide of interest may be further purified using chromatographic and electrophoretic techniques to achieve partial or complete purification (or purification to homogeneity).
  • Analytical methods particularly suited to the preparation of a pure peptide are ion-exchange chromatography, gel exclusion chromatography, polyacrylamide gel electrophoresis, affinity chromatography, immunoaffinity chromatography and isoelectric focusing.
  • An example of receptor protein purification by affinity chromatography is disclosed in U.S. Patent No. 5,206,347 , the entire text of which is incorporated herein by reference.
  • a particularly efficient method of purifying peptides is fast protein liquid chromatography (FPLC) or even HPLC.
  • a purified protein or peptide is intended to refer to a composition, isolatable from other components, wherein the protein or peptide is purified to any degree relative to its naturally-obtainable state.
  • An isolated or purified protein or peptide therefore, also refers to a protein or peptide free from the environment in which it may naturally occur.
  • purified will refer to a protein or peptide composition that has been subjected to fractionation to remove various other components, and which composition substantially retains its expressed biological activity.
  • substantially purified this designation will refer to a composition in which the protein or peptide forms the major component of the composition, such as constituting about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, or more of the proteins in the composition.
  • Various methods for quantifying the degree of purification of the protein or peptide are known to those of skill in the art in light of the present disclosure. These include, for example, determining the specific activity of an active fraction, or assessing the amount of polypeptides within a fraction by SDS/PAGE analysis.
  • a preferred method for assessing the purity of a fraction is to calculate the specific activity of the fraction, to compare it to the specific activity of the initial extract, and to thus calculate the degree of purity therein, assessed by a "-fold purification number.”
  • the actual units used to represent the amount of activity will, of course, be dependent upon the particular assay technique chosen to follow the purification, and whether or not the expressed protein or peptide exhibits a detectable activity.
  • Partial purification may be accomplished by using fewer purification steps in combination, or by utilizing different forms of the same general purification scheme. For example, it is appreciated that a cation-exchange column chromatography performed utilizing an HPLC apparatus will generally result in a greater "-fold" purification than the same technique utilizing a low pressure chromatography system. Methods exhibiting a lower degree of relative purification may have advantages in total recovery of protein product, or in maintaining the activity of an expressed protein.
  • Affinity chromatography is a chromatographic procedure that relies on the specific affinity between a substance to be isolated and a molecule to which it can specifically bind to. This is a receptor-ligand type of interaction.
  • the column material is synthesized by covalently coupling one of the binding partners to an insoluble matrix. The column material is then able to specifically adsorb the substance from the solution. Elution occurs by changing the conditions to those in which binding will not occur ( e . g ., altered pH, ionic strength, temperature, etc .).
  • the matrix should be a substance that itself does not adsorb molecules to any significant extent and that has a broad range of chemical, physical and thermal stability.
  • the ligand should be coupled in such a way as to not affect its binding properties. The ligand should also provide relatively tight binding. And it should be possible to elute the substance without destroying the sample or the ligand.
  • the targeting peptides of the invention can be synthesized in solution or on a solid support in accordance with conventional techniques.
  • Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Stewart and Young, (1984); Tam et al ., (1983); Merrifield, (1986); and Barany and Merrifield (1979), each incorporated herein by reference. Short peptide sequences, usually from about 6 up to about 35 to 50 amino acids, can be readily synthesized by such methods.
  • recombinant DNA technology may be employed wherein a nucleotide sequence which encodes a peptide of the invention is inserted into an expression vector, transformed or transfected into an appropriate host cell, and cultivated under conditions suitable for expression.
  • the appropriate targeting peptide or receptor, or portions thereof may be coupled, bonded, bound, conjugated, or chemically-linked to one or more agents via linkers, polylinkers, or derivatized amino acids. This may be performed such that a bispecific or multivalent composition or vaccine is produced. It is further envisioned that the methods used in the preparation of these compositions are familiar to those of skill in the art and should be suitable for administration to humans, i . e ., pharmaceutically acceptable.
  • Preferred agents are the carriers are keyhole limpet hemocyanin (KLH) or bovine serum albumin (BSA).
  • antibody is used to refer to any antibody-like molecule that has an antigen binding region, and includes antibody fragments such as Fab', Fab, F(ab') 2 , single domain antibodies (DABs), Fv, scFv (single chain Fv), and the like. Techniques for preparing and using various antibody-based constructs and fragments are well known in the art. Means for preparing and characterizing antibodies are also well known in the art (See, e . g ., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988 ; incorporated herein by reference).
  • cytokine is a generic term for proteins released by one cell population which act on another cell as intercellular mediators. Examples of such cytokines are lymphokines, monokines, growth factors and traditional polypeptide hormones.
  • cytokines include growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); hepatic growth factor; prostaglandin, fibroblast growth factor; prolactin; placental lactogen, OB protein; tumor necrosis factor-.alpha.
  • growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone
  • parathyroid hormone such as thyroxine
  • insulin proinsulin
  • relaxin prorelaxin
  • glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH)
  • FSH follicle stimulating hormone
  • TSH thyroid stimulating hormone
  • LH luteinizing hormone
  • TGFs transforming growth factors
  • CSFs colony stimulating factors
  • M-CSF macrophage-CSF
  • GM-CSF granulocyte-macrophage-CSF
  • G-CSF granulocyte-CSF
  • ILs interleukins
  • Chemokines generally act as chemoattractants to recruit immune effector cells to the site of chemokine expression. It may be advantageous to express a particular chemokine gene in combination with, for example, a cytokine gene, to enhance the recruitment of other immune system components to the site of treatment. Chemokines include, but are not limited to, RANTES, MCAF, MIP1-alpha, MIP1-Beta, and IP-10. The skilled artisan will recognize that certain cytokines are also known to have chemoattractant effects and could also be classified under the term chemokines.
  • the claimed peptides or proteins of the present invention may be attached to imaging agents of use for imaging and diagnosis of various diseased organs, tissues or cell types.
  • imaging agents are known in the art, as are methods for their attachment to proteins or peptides (see, e . g ., U.S. patents 5,021,236 and 4,472,509 , both incorporated herein by reference).
  • Certain attachment methods involve the use of a metal chelate complex employing, for example, an organic chelating agent such a DTPA attached to the protein or peptide ( U.S. Patent 4,472,509 ).
  • Proteins or peptides also may be reacted with an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate.
  • a coupling agent such as glutaraldehyde or periodate.
  • Conjugates with fluorescein markers are prepared in the presence of these coupling agents or by reaction with an isothiocyanate.
  • Non-limiting examples of paramagnetic ions of potential use as imaging agents include chromium (I11), manganese (II), iron (III), iron (II), cobalt (II), nickel (II), copper (II), neodymium (III), samarium (III), ytterbium (III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) and erbium (III), with gadolinium being particularly preferred.
  • Ions useful in other contexts, such as X-ray imaging include but are not limited to lanthanum (III), gold (III), lead (II), and especially bismuth (III).
  • Radioisotopes of potential use as imaging or therapeutic agents include astatine 211 , 14 carbon, 51 chromium, 36 chlorine, 57 cobalt, 58 cobalt, copper 67 , 152 Eu, gallium 67 , 3 hydrogen, iodine 123 , iodine 125 , iodine 131 , indium 111 , 59 iron , 32 phosphorus, rhenium 186 , rhenium 188 , 75 selenium, 35 sulphur, technicium 99m and yttrium 90 .
  • 125 I is often being preferred for use in certain embodiments, and technicium 99m and indium 111 are also often preferred due to their low energy and suitability for long range detection.
  • Radioactively labeled proteins or peptides of the present invention may be produced according to well-known methods in the art. For instance, they can be iodinated by contact with sodium or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase. Proteins or peptides according to the invention may be labeled with technetium- 99m by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the peptide to this column or by direct labeling techniques, e .
  • ligand exchange process for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the peptide to this column or by direct labeling techniques, e .
  • a reducing agent such as SNCl 2
  • a buffer solution such as sodium-potassium phthalate solution
  • Intermediary functional groups which are often used to bind radioisotopes which exist as metallic ions to peptides are diethylenetriaminepentaacetic acid (DTPA) and ethylene diaminetetracetic acid (EDTA).
  • fluorescent labels including rhodamine, fluorescein isothiocyanate and renographin.
  • the claimed proteins or peptides may be linked to a secondary binding ligand or to an enzyme (an enzyme tag) that will generate a colored product upon contact with a chromogenic substrate.
  • suitable enzymes include urease, alkaline phosphatase, (horseradish) hydrogen peroxidase and glucose oxidase.
  • Preferred secondary binding ligands are biotin and avidin or streptavidin compounds. The use of such labels is well known to those of skill in the art in light and is described, for example, in U.S. Patents 3,817,837 ; 3,850,752 ; 3,939,350 ; 3,996,345 ; 4,277,437 ; 4,275,149 and 4,366,241 ; each incorporated herein by reference.
  • Bifunctional cross-linking reagents have been extensively used for a variety of purposes including preparation of affinity matrices, modification and stabilization of diverse structures, identification of ligand and receptor binding sites, and structural studies. Homobifunctional reagents that carry two identical functional groups proved to be highly efficient in inducing cross-linking between identical and different macromolecules or subunits of a macromolecule, and linking of polypeptide ligands to their specific binding sites. Heterobifunctional reagents contain two different functional groups. By taking advantage of the differential reactivities of the two different functional groups, cross-linking can be controlled both selectively and sequentially. The bifunctional cross-linking reagents can be divided according to the specificity of their functional groups, e .
  • reagents directed to free amino groups have become especially popular because of their commercial availability, ease of synthesis and the mild reaction conditions under which they can be applied.
  • a majority of heterobifunctional cross-linking reagents contains a primary amine-reactive group and a thiol-reactive group.
  • ligands can be covalently bound to liposomal surfaces through the cross-linking of amine residues.
  • Liposomes in particular, multilamellar vesicles (MLV) or unilamellar vesicles such as microemulsified liposomes (MEL) and large unilamellar liposomes (LUVET), each containing phosphatidylethanolamine (PE), have been prepared by established procedures.
  • MLV multilamellar vesicles
  • MEL microemulsified liposomes
  • LVET large unilamellar liposomes
  • PE in the liposome provides an active functional residue, a primary amine, on the liposomal surface for cross-linking purposes.
  • Ligands such as epidermal growth factor (EGF) have been successfully linked with PE-liposomes. Ligands are bound covalently to discrete sites on the liposome surfaces. The number and surface density of these sites are dictated by the liposome formulation and the liposome type. The liposomal surfaces may also have sites for non-covalent association.
  • cross-linking reagents have been studied for effectiveness and biocompatibility.
  • Cross-linking reagents include glutaraldehyde (GAD), bifunctional oxirane (OXR), ethylene glycol diglycidyl ether (EGDE), and a water soluble carbodiimide, preferably 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC).
  • GAD glutaraldehyde
  • OXR bifunctional oxirane
  • EGDE ethylene glycol diglycidyl ether
  • EDC 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide
  • heterobifunctional cross-linking reagents and methods of using the cross-linking reagents are described ( U.S. Patent 5,889,155 , specifically incorporated herein by reference in its entirety).
  • the cross-linking reagents combine a nucleophilic hydrazide residue with an electrophilic maleimide residue, allowing coupling in one example, of aldehydes to free thiols.
  • the cross-linking reagent can be modified to cross-link various functional groups.
  • Nucleic acids according to the present invention may encode a targeting peptide, a receptor protein or a fusion protein.
  • the nucleic acid may be derived from genomic DNA, complementary DNA (cDNA) or synthetic DNA. Where incorporation into an expression vector is desired, the nucleic acid may also comprise a natural intron or an intron derived from another gene. Such engineered molecules are sometime referred to as "mini-genes.”
  • nucleic acid as used herein includes single-stranded and double-stranded molecules, as well as DNA, RNA, chemically modified nucleic acids and nucleic acid analogs. It is contemplated that a nucleic acid within the scope of the present invention may be of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,
  • targeting peptides, fusion proteins and receptors may be encoded by any nucleic acid sequence that encodes the appropriate amino acid sequence.
  • the design and production of nucleic acids encoding a desired amino acid sequence is well known to those of skill in the art, using standardized codon tables (see Table 2 below).
  • the codons selected for encoding each amino acid may be modified to optimize expression of the nucleic acid in the host cell of interest. Codon preferences for various species of host cell are well known in the art.
  • the present invention encompasses complementary nucleic acids that hybridize under high stringency conditions with such coding nucleic acid sequences.
  • High stringency conditions for nucleic acid hybridization are well known in the art.
  • conditions may comprise low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50°C to about 70°C.
  • the temperature and ionic strength of a desired stringency are determined in part by the length of the particular nucleic acid(s), the length and nucleotide content of the target sequence(s), the charge composition of the nucleic acid(s), and to the presence or concentration of formamide, tetramethylammonium chloride or other solvent(s) in a hybridization mixture.
  • expression vectors are employed to express the targeting peptide or fusion protein, which can then be purified and used.
  • the expression vectors are used in gene therapy. Expression requires that appropriate signals be provided in the vectors, and which include various regulatory elements, such as enhancers/promoters from both viral and mammalian sources that drive expression of the genes of interest in host cells. Elements designed to optimize messenger RNA stability and translatability in host cells also are known.
  • expression construct or "expression vector” are meant to include any type of genetic construct containing a nucleic acid coding for a gene product in which part or all of the nucleic acid coding sequence is capable of being transcribed.
  • the nucleic acid encoding a gene product is under transcriptional control of a promoter.
  • a “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a gene.
  • under transcriptional control means that the promoter is in the correct location and orientation in relation to the nucleic acid to control RNA polymerase initiation and expression of the gene.
  • the particular promoter employed to control the expression of a nucleic acid sequence of interest is not believed to be important, so long as it is capable of directing the expression of the nucleic acid in the targeted cell.
  • a human cell it is preferable to position the nucleic acid coding region adjacent and under the control of a promoter that is capable of being expressed in a human cell.
  • a promoter might include either a human or viral promoter.
  • the human cytomegalovirus (CMV) immediate early gene promoter can be used to obtain high-level expression of the coding sequence of interest.
  • CMV cytomegalovirus
  • the use of other viral or mammalian cellular or bacterial phage promoters which are well-known in the art to achieve expression of a coding sequence of interest is contemplated as well, provided that the levels of expression are sufficient for a given purpose.
  • a cDNA insert typically one will typically include a polyadenylation signal to effect proper polyadenylation of the gene transcript.
  • the nature of the polyadenylation signal is not believed to be crucial to the successful practice of the invention, and any such sequence may be employed, such as human growth hormone and SV40 polyadenylation signals.
  • a terminator also contemplated as an element of the expression construct. These elements can serve to enhance message levels and to minimize read through from the construct into other sequences.
  • the cells containing nucleic acid constructs of the present invention may be identified in vitro or in vivo by including a marker in the expression construct.
  • a marker in the expression construct.
  • Such markers would confer an identifiable change to the cell permitting easy identification of cells containing the expression construct.
  • a drug selection marker aids in cloning and in the selection of transformants.
  • genes that confer resistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin, and histidinol are useful selectable markers.
  • enzymes such as herpes simplex virus thymidine kinase ( tk ) or chloramphenicol acetyltransferase (CAT) may be employed.
  • Immunologic markers also can be employed.
  • the selectable marker employed is not believed to be important, so long as it is capable of being expressed simultaneously with the nucleic acid encoding a gene product. Further examples of selectable markers are well known to one of skill in the art
  • the expression construct comprises a virus or engineered construct derived from a viral genome.
  • Preferred gene therapy vectors are generally viral vectors.
  • viruses that can accept foreign genetic material are limited in the number of nucleotides they can accommodate and in the range of cells they infect, these viruses have been demonstrated to successfully effect gene expression.
  • adenoviruses do not integrate their genetic material into the host genome and therefore do not require host replication for gene expression making them ideally suited for rapid, efficient, heterologous gene expression. Techniques for preeparing replication infective viruses are well known in the art.
  • a preferred means of purifying the vector involves the use of buoyant density gradients, such as cesium chloride gradient centrifugation.
  • DNA viruses used as gene vectors include the papovaviruses (e . g ., simian virus 40, bovine papilloma virus, and polyoma) (Ridgeway, 1988; Baichwal and Sugden, 1986) and adenoviruses (Ridgeway, 1988; Baichwal and Sugden, 1986).
  • papovaviruses e . g ., simian virus 40, bovine papilloma virus, and polyoma
  • adenoviruses Rosgeway, 1988; Baichwal and Sugden, 1986.
  • adenovirus expression vector is meant to include, but is not limited to, constructs containing adenovirus sequences sufficient to (a) support packaging of the construct and (b) to express an antisense or a sense polynucleotide that has been cloned therein.
  • the expression vector comprises a genetically engineered form of adenovirus.
  • retroviral infection the adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner without potential genotoxicity.
  • adenoviruses are structurally stable, and no genome rearrangement has been detected after extensive amplification. Adenovirus can infect virtually all epithelial cells regardless of their cell cycle stage. So far, adenoviral infection appears to be linked only to mild disease such as acute respiratory disease in humans.
  • Adenovirus is particularly suitable for use as a gene transfer vector because of its mid-sized genome, ease of manipulation, high titer, wide target cell range and high infectivity. Both ends of the viral genome contain 100-200 base pair inverted repeats (ITRs), which are cis elements necessary for viral DNA replication and packaging.
  • ITRs inverted repeats
  • the early (E) and late (L) regions of the genome contain different transcription units that are divided by the onset of viral DNA replication.
  • the E1 region (E1A and E1B) encodes proteins responsible for the regulation of transcription of the viral genome and a few cellular genes.
  • the expression of the E2 region results in the synthesis of the proteins for viral DNA replication.
  • MLP major late promoter
  • TPL 5'-tripartite leader
  • recombinant adenovirus is generated from homologous recombination between shuttle vector and provirus vector. Due to the possible recombination between two proviral vectors, wild-type adenovirus may be generated from this process. Therefore, it is critical to isolate a single clone of virus from an individual plaque and examine its genomic structure.
  • adenovirus vectors which are replication deficient depend on a unique helper cell line, designated 293, which is transformed from human embryonic kidney cells by Ad5 DNA fragments and constitutively expresses E1 proteins (Graham et al ., 1977). Since the E3 region is dispensable from the adenovirus genome (Jones and Shenk, 1978), the current adenovirus vectors, with the help of 293 cells, carry foreign DNA in either the E1, the E3, or both regions (Graham and Prevec, 1991). In nature, adenovirus can package approximately 105% of the wild-type genome (Ghosh-Choudhury et al ., 1987), providing capacity for about 2 extra kb of DNA.
  • the maximum capacity of the current adenovirus vector is under 7.5 kb, or about 15% of the total length of the vector. More than 80% of the adenovirus viral genome remains in the vector backbone and is the source of vector-borne cytotoxicity. Also, the replication deficiency of the E1-deleted virus is incomplete. For example, leakage of viral gene expression has been observed with the currently available vectors at high multiplicities of infection (MOI) (Mulligan, 1993).
  • MOI multiplicities of infection
  • Helper cell lines may be derived from human cells such as human embryonic kidney cells, muscle cells, hematopoietic cells or other human embryonic mesenchymal or epithelial cells.
  • the helper cells may be derived from the cells of other mammalian species that are permissive for human adenovirus. Such cells include, e . g ., Vero cells or other monkey embryonic mesenchymal or epithelial cells.
  • the preferred helper cell line is 293.
  • Racher et al ., (1995) disclosed improved methods for culturing 293 cells and propagating adenovirus.
  • natural cell aggregates are grown by inoculating individual cells into 1 liter siliconized spinner flasks (Techne, Cambridge, UK) containing 100-200 m1 of medium. Following stirring at 40 rpm, the cell viability is estimated with trypan blue.
  • Fibra-Cel microcarriers (Bibby Sterlin, Stone, UK) (5 g/l) are employed as follows.
  • a cell innoculum, resuspended in 5 ml of medium, is added to the carrier (50 ml) in a 250 ml Erlenmeyer flask and left stationary, with occasional agitation, for 1 to 4 h.
  • the medium is then replaced with 50 ml of fresh medium and shaking is initiated.
  • cells are allowed to grow to about 80% confluence, after which time the medium is replaced (to 25% of the final volume) and adenovirus added at an MOI of 0.05. Cultures are left stationary overnight, following which the volume is increased to 100% and shaking is commenced for another 72 hr.
  • the adenovirus may be of any of the 42 different known serotypes or subgroups A-F.
  • Adenovirus type 5 of subgroup C is the preferred starting material in order to obtain the conditional replication-defective adenovirus vector for use in the present invention. This is because Adenovirus type 5 is a human adenovirus about which a great deal of biochemical and genetic information is known, and it has historically been used for most constructions employing adenovirus as a vector.
  • a typical vector applicable to practicing the present invention is replication defective and will not have an adenovirus E1 region.
  • the position of insertion of the construct within the adenovirus sequences is not critical.
  • the polynucleotide encoding the gene of interest may also be inserted in lieu of the deleted E3 region in E3 replacement vectors as described by Karlsson et al ., (1986) or in the E4 region where a helper cell line or helper virus complements the E4 defect.
  • Adenovirus is easy to grow and manipulate and exhibits broad host range in vitro and in vivo. This group of viruses can be obtained in high titers, e . g ., 10 9 -10 11 plaque-forming units per ml, and they are highly infective. The life cycle of adenovirus does not require integration into the host cell genome. The foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. No side effects have been reported in studies of vaccination with wild-type adenovirus (Couch et al ., 1963; Top et al ., 1971), demonstrating their safety and therapeutic potential as in vivo gene transfer vectors.
  • Adenovirus vectors have been used in eukaryotic gene expression (Levrero et al ., 1991; Gomez-Foix et al ., 1992) and vaccine development (Grunhaus and Horwitz, 1992; Graham and Prevec, 1991). Animal studies have suggested that recombinant adenovirus could be used for gene therapy (Stratford-Perricaudet and Perricaudet, 1991; Stratford-Perricaudet et al ., 1990; Rich et al ., 1993).
  • retroviruses are a group of single-stranded RNA viruses characterized by an ability to convert their RNA to double-stranded DNA in infected cells by a process of reverse-transcription (Coffin, 1990).
  • the resulting DNA then stably integrates into cellular chromosomes as a provirus and directs synthesis of viral proteins.
  • the integration results in the retention of the viral gene sequences in the recipient cell and its descendants.
  • the retroviral genome contains three genes, gag , pol , and env . that code for capsid proteins, polymerase enzyme, and envelope components, respectively.
  • a sequence found upstream from the gag gene contains a signal for packaging of the genome into virions.
  • Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences, and also are required for integration in the host cell genome (Coffin, 1990).
  • a nucleic acid encoding protein of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective.
  • Retroviral vectors are capable of infecting a broad variety of cell types. However, integration and stable expression require the division of host cells (Paskind et al ., 1975).
  • retrovirus vectors usually integrate into random sites in the cell genome. This can lead to insertional mutagenesis through the interruption of host genes or through the insertion of viral regulatory sequences that can interfere with the function of flanking genes (Varmus et al ., 1981).
  • Another concern with the use of defective retrovirus vectors is the potential appearance of wild-type replication-competent virus in the packaging cells. This may result from recombination events in which the intact sequence from the recombinant virus inserts upstream from the gag, pol , env sequence integrated in the host cell genome.
  • new packaging cell lines are now available that should greatly decrease the likelihood of recombination (Markowitz et al ., 1988; Hersdorffer et al ., 1990).
  • viral vectors may be employed as expression constructs.
  • Vectors derived from viruses such as vaccinia virus (Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al ., 1988), adeno-associated virus (AAV) (Ridgeway, 1988; Baichwal and Sugden, 1986; Hermonat and Muzycska, 1984), and herpes viruses may be employed. They offer several attractive features for various mammalian cells (Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al ., 1988; Horwich et al ., 1990).
  • Non-viral methods for the transfer of expression constructs into cultured mammalian cells include calcium phosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al ., 1990), DEAE-dextran (Gopal, 1985), electroporation (Tur-Kaspa et al ., 1986; Potter et al ., 1984), direct microinjection, DNA-loaded liposomes and lipofectamine-DNA complexes, cell sonication, gene bombardment using high velocity microprojectiles, and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988). Some of these techniques may be successfully adapted for in vivo or ex vivo use.
  • the expression construct may be entrapped in a liposome.
  • Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers. Also contemplated are lipofectamine-DNA complexes.
  • Liposome-mediated nucleic acid delivery and expression of foreign DNA in vitro has been very successful.
  • Wong et al ., (1980) demonstrated the feasibility of liposome-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa, and hepatoma cells.
  • Nicolau et al ., (1987) accomplished successful liposome-mediated gene transfer in rats after intravenous injection.
  • a number of selection systems may be used including, but not limited to, HSV thymidine kinase, hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase genes, in tk- , hgprt- or aprt- cells, respectively.
  • antimetabolite resistance can be used as the basis of selection for dhfr: that confers resistance to methotrexate; gpt , that confers resistance to mycophenolic acid; neo , that confers resistance to the aminoglycoside G418; and hygro , that confers resistance to hygromycin.
  • compositions - expression vectors, virus stocks, proteins, antibodies and drugs - it may be necessary to prepare pharmaceutical compositions - expression vectors, virus stocks, proteins, antibodies and drugs - in a form appropriate for the intended application. Generally, this will entail preparing compositions that are essentially free of impurities that could be harmful to humans or animals.
  • Aqueous compositions of the present invention comprise an effective amount of the protein or peptide, dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium. Such compositions also are referred to as innocula.
  • pharmaceutically or pharmacologically acceptable refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human.
  • pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the proteins or peptides of the present invention, its use in therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.
  • compositions of the present invention may include classic pharmaceutical preparations. Administration of these compositions according to the present invention are via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, rectal, vaginal or topical. Alternatively, administration may be by orthotopic, intradermal, subcutaneous, intramuscular, intraperitoneal, intraarterial or intravenous injection. Such compositions normally would be administered as pharmaceutically acceptable compositions, described supra .
  • the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • a coating such as lecithin
  • surfactants for example, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium bicarbonate, sodium sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various other ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • chemotherapeutic agents may be attached to a targeting peptide or fusion protein for selective delivery to a tumor.
  • Agents or factors suitable for use may include any chemical compound that induces DNA damage when applied to a cell.
  • Chemotherapeutic agents include, but are not limited to, 5-fluorouracil, bleomycin, busulfan, camptothecin, carboplatin, chlorambucil, cisplatin (CDDP), cyclophosphamide, dactinomycin, daunorubicin, doxorubicin, estrogen receptor binding agents, etoposide (VP16), farnesyl-protein transferase inhibitors, gemcitabine, ifosfamide, mechlorethamine, melphalan, mitomycin, navelbine, nitrosurea, plicomycin, procarbazine, raloxifene, tamoxifen, taxol, temazolomide (an aqueous form of DTIC), transplatinum
  • chemotherapeutic agents fall into the following categories: alkylating agents, antimetabolites, antitumor antibiotics, corticosteroid hormones, mitotic inhibitors, and nitrosoureas, hormone agents, miscellaneous agents, and any analog or derivative variant thereof.
  • Chemotherapeutic agents and methods of administration, dosages, etc. are well known to those of skill in the art (see for example, the “Physicians Desk Reference”, Goodman & Gilman's “The Pharmacological Basis of Therapeutics” and in “Remington's Pharmaceutical Sciences", incorporated herein by reference in relevant parts), and may be combined with the invention in light of the disclosures herein. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Examples of specific chemotherapeutic agents and dose regimes are also described herein.
  • Alkylating agents are drugs that directly interact with genomic DNA to prevent the cancer cell from proliferating. This category of chemotherapeutic drugs represents agents that affect all phases of the cell cycle, that is, they are not phase-specific.
  • An alkylating agent may include, but is not limited to, a nitrogen mustard, an ethylenimene, a methylmelamine, an alkyl sulfonate, a nitrosourea or a triazines. They include but are not limited to: busulfan, chlorambucil, cisplatin, cyclophosphamide (cytoxan), dacarbazine, ifosfamide, mechlorethamine (mustargen), and melphalan.
  • Antimetabolites disrupt DNA and RNA synthesis. Unlike alkylating agents, they specifically influence the cell cycle during S phase. Antimetabolites can be differentiated into various categories, such as folic acid analogs, pyrimidine analogs and purine analogs and related inhibitory compounds. Antimetabolites include but are not limited to, 5-fluorouracil (5-FU), cytarabine (Ara-C), fludarabine, gemcitabine, and methotrexate.
  • 5-FU 5-fluorouracil
  • Ara-C cytarabine
  • fludarabine gemcitabine
  • gemcitabine gemcitabine
  • methotrexate methotrexate
  • Natural products generally refer to compounds originally isolated from a natural source, and identified has having a pharmacological activity. Such compounds, analogs and derivatives thereof may be, isolated from a natural source, chemically synthesized or recombinantly produced by any technique known to those of skill in the art. Natural products include such categories as mitotic inhibitors, antitumor antibiotics, enzymes and biological response modifiers.
  • Mitotic inhibitors include plant alkaloids and other natural agents that can inhibit either protein synthesis required for cell division or mitosis. They operate during a specific phase during the cell cycle. Mitotic inhibitors include, for example, docetaxel, etoposide (VP16), teniposide, paclitaxel, taxol, vinblastine, vincristine, and vinorelbine.
  • Mitotic inhibitors include, for example, docetaxel, etoposide (VP16), teniposide, paclitaxel, taxol, vinblastine, vincristine, and vinorelbine.
  • Taxoids are a class of related compounds isolated from the bark of the ash tree, Taxus brevifolia. Taxoids include but are not limited to compounds such as docetaxel and paclitaxel. Paclitaxel binds to tubulin (at a site distinct from that used by the vinca alkaloids) and promotes the assembly of microtubules.
  • Vinca alkaloids are a type of plant alkaloid identified to have pharmaceutical activity. They include such compounds as vinblastine (VLB) and vincristine.
  • Antitumor antibiotics have both antimicrobial and cytotoxic activity. These drugs also interfere with DNA by chemically inhibiting enzymes and mitosis or altering cellular membranes. These agents are not phase specific so they work in all phases of the cell cycle. Examples of antitumor antibiotics include, but are not limited to, bleomycin, dactinomycin, daunorubicin, doxorubicin (Adriamycin), plicamycin (mithramycin) and idarubicin.
  • Corticosteroid hormones are considered chemotherapy drugs when they are implemented to kill or slow the growth of cancer cells. Corticosteroid hormones can increase the effectiveness of other chemotherapy agents, and consequently, they are frequently used in combination treatments. Prednisone and dexamethasone are examples of corticosteroid hormones.
  • Progestins such as hydroxyprogesterone caproate, medroxyprogesterone acetate, and megestrol acetate have been used in cancers of the endometrium and breast.
  • Estrogens such as diethylstilbestrol and ethinyl estradiol have been used in cancers such as breast and prostate.
  • Antiestrogens such as tamoxifen have been used in cancers such as breast.
  • Androgens such as testosterone propionate and fluoxymesterone have also been used in treating breast cancer.
  • Antiandrogens such as flutamide have been used in the treatment of prostate cancer.
  • Gonadotropin-releasing hormone analogs such as leuprolide have been used in treating prostate cancer.
  • Some chemotherapy agents do not fall into the previous categories based on their activities. They include, but are not limited to, platinum coordination complexes, anthracenedione, substituted urea, methyl hydrazine derivative, adrenalcortical suppressant, amsacrine, L-asparaginase, and tretinoin. It is contemplated that they may be used within the compositions and methods of the present invention.
  • Platinum coordination complexes include such compounds as carboplatin and cisplatin ( cis-DDP ).
  • An anthracenedione such as mitoxantrone has been used for treating acute granulocytic leukemia and breast cancer.
  • a substituted urea such as hydroxyurea has been used in treating chronic granulocytic leukemia, polycythemia vera, essental thrombocytosis and malignant melanoma.
  • a methyl hydrazine derivative such as procarbazine (N-methylhydrazine, MIH) has been used in the treatment of Hodgkin's disease.
  • An adrenocortical suppressant such as mitotane has been used to treat adrenal cortex cancer, while aminoglutethimide has been used to treat Hodgkin's disease.
  • Apoptosis or programmed cell death, is an essential process for normal embryonic development, maintaining homeostasis in adult tissues, and suppressing carcinogenesis (Kerr et al., 1972).
  • the Bcl-2 family of proteins and ICE-like proteases have been demonstrated to be important regulators and effectors of apoptosis in other systems.
  • the Bcl-2 protein plays a prominent role in controlling apoptosis and enhancing cell survival in response to diverse apoptotic stimuli (Bakhshi et al., 1985; Cleary and Sklar, 1985; Cleary et al., 1986; Tsujimoto et al., 1985; Tsujimoto and Croce, 1986).
  • the evolutionarily conserved Bcl-2 protein now is recognized to be a member of a family of related proteins, which can be categorized as death agonists or death antagonists.
  • Bcl-2 acts to suppress cell death triggered by a variety of stimuli. Also, it now is apparent that there is a family of Bcl-2 cell death regulatory proteins which share in common structural and sequence homologies. These different family members have been shown to either possess similar functions to Bcl-2 (e.g., Bcl XL , Bcl W , Bcl S , Mcl-1, A1, Bfl-1) or counteract Bcl-2 function and promote cell death (e.g., Bax, Bak, Bik, Bim, Bid, Bad, Harakiri).
  • Non-limiting examples of pro-apoptosis agents contemplated within the scope of the present invention include gramicidin, magainin, mellitin, defensin, cecropin, (KLAKLAK) 2 (SEQ ID NO:1), (KLAKKLA) 2 (SEQ ID NO:2), (KAAKKAA) 2 (SEQ ID NO:3) or (KLGKKLG) 3 (SEQ ID NO:4).
  • the present invention may concern administration of targeting peptides attached to anti-angiogenic agents, such as angiotensin, laminin peptides, fibronectin peptides, plasminogen activator inhibitors, tissue metalloproteinase inhibitors, interferons, interleukin 12, platelet factor 4, IP-10, Gro- ⁇ , thrombospondin, 2-methoxyoestradiol, proliferin-related protein, carboxiamidotriazole, CM101, Marimastat, pentosan polysulphate, angiopoietin 2 (Regeneron), interferon-alpha, herbimycin A, PNU145156E, 16K prolactin fragment, Linomide, thalidomide, pentoxifylline, genistein, TNP-470, endostatin, paclitaxel, accutin, angiostatin, cidofovir, vincristine, bleomycin, AGM-1470, plate
  • Bone is the preferred site of metastasis in the large majority of patients with prostate cancer (Fidler, 1999). This striking selectivity has been viewed as an example of site-specific interactions that were essential to cancer progression (Rak, 1995; Zetter, 1998). Despite the clinical relevance, little is known about the mechanisms that control prostate cancer spread to bone. In addition, there were no effective strategies for targeting therapeutic agents for the treatment of metastatic prostate cancer (Brodt et. al, 1996).
  • a subset of peptides capable of selective homing to bone marrow through the circulation is likely to simulate the behavior of prostate cancer cells during bone metastasis formation.
  • the vascular markers targeted by using phage display might also be utilized by tumor cells to metastasize. This concept has already been proven to be true for lung-homing peptides. Peptides that home to lung blood vessels inhibit experimental metastasis. These results fit a "modified seed and soil" model, in which the basis for site-specific metastasis is the presence of homing receptors in blood vessels of certain tissues to which metastasis preferentially occurs.
  • Such selective vascular markers are exposed to tumor cells during adhesion, the first step of the metastastic cascade.
  • Isolation of bone marrow-homing peptides is of utility for identifying those vascular markers that mediate prostate cancer cell homing during the metastatic process, and for potential therapeutic intervention in preventing metastases to bone, or in selectively imaging and/or treating cancer that has already metastasized to bone.
  • Phage libraries were injected intravenously.
  • the libraries were prepared according to the protocol of Smith and Scott (1985) with improvements, discussed below.
  • the phage in these libraries displayed inserts ranging from 5 to 11 residues.
  • Tissue samples were processed for phage rescue by transfer to 1ml DMEM-PI in a glass tube and homogenized with a grinder. Bone marrow does not require homogenization, whereas other organs that were used as controls needed to be minced before they could be efficiently homogenized.
  • Samples were transferred to autoclaved 2 ml Eppendorf tubes. The tissues were washed with ice cold DMEM-PI containing 1% BSA. After 3 washes, the pellets were resuspended and brought to 37°C before adding bacteria. Incubation of the washed tissue samples with 1.5 ml of competent K91-kan bacteria (OD 600 0.2 in 1:10 dil.) for one hour at room temperature was used for recovering the phage particles.
  • the remaining 2 -3 ml of infected culture (including the homogenized tissue) was transferred into 10 ml of LB medium containing 40 ⁇ g/ml tetracycline and 100 ⁇ g/ml kanamycin (LB tet/kan) and placed in the shaker at 37°C for 2h.
  • the 12 ml cultures were expanded to 1 liter LB tet/kan and grown overnight in the 37°C shaker. Phage were rescued from the bulk amplified bacterial culture after 12-16 h, according to standard protocols and saved for subsequent rounds of selection. From the plates/dishes in the incubator, well separated colonies from bone marrow were sequenced. The colonies were transferred to 96 well plates containing 20 ⁇ l PBS/well for sequencing
  • Immunohistochemical staining with an anti-M13 antibody was used to examine phage targeting in various tissues (Pasqualini and Ruoslahti, 1996; Arap et al, 1998).
  • the phage were injected IV and allowed to circulate for 5 min or 24 h. Mice in the 5 min experiment were perfused with DMEM after the phage injection to remove unbound phage from the circulation. There was little circulating phage after 24 h (Arap et al, 1998a, 1998b).
  • the animals were sacrificed, their tissues collected, fixed with Bouin's solution, sectioned and stained with antibodies against the phage.
  • Bone marrow targeting sequence motifs were identified by intravenously injecting phage libraries into mice and recovering phage from bone marrow. Phage were injected intravenously, recovered from the bone marrow, repeatedly amplified in vitro and re-injected to obtain sufficient enrichment. After three rounds of selection, phage preparations that homed to mouse bone marrow were obtained. The individual phage exhibited similar organ specificity as the pooled phage after intravenous injection. Several peptide motifs were identified and characterized. The most promising motifs that show specificity in vivo are shown in Table 3 Table 3. Sequences in phage that target murine bone marrow in vivo.
  • bone marrow targeting peptide sequences identified herein will be of use for numerous applications within the scope of the present invention, including but not limited to targeted delivery of therapeutic agents or gene therapy, in vivo imaging of normal or diseased organs, tissues or cell types, identification of receptors and receptor ligands in organs, tissues or cell types, and therapeutic treatment of a number of human diseases, particularly metastatic prostate cancer.
  • Prostate is an unusual organ because it continues to growth throughout adult life.
  • benign prostate hypertrophy (BPH) affects most elderly men to some degree.
  • BPH benign prostate hypertrophy
  • the prostate is a frequent site of malignant tumors.
  • serum markers for prostate cancer were available, many of these malignant tumors were currently detected early in the course of the disease.
  • many were aggressively treated with surgery or radiotherapy often with devastating side-effects such as incontinence and impotence (Lane and Shah, 1999; Mikolajczyk et al., 2000).
  • the methods of the present invention allow the identification of peptides that home to specific target sites in vivo (Pasqualini et al., 1996, 1997, Koivunen et al., 1999; Pasqualini, 1999). In vivo selection of phage peptide libraries yields peptides that are capable of homing to specific receptors in target tissues through the circulation. These studies have revealed a surprising degree of specialization in various normal tissues (Pasqualini, 1999; Rajotte et al., 1998, 1999). The present example concerns compositions and methods of use of prostate targeting peptides.
  • Phage display libraries were injected intravenously. Samples were kept on ice at all times. Prostate tissue samples were processed as follows. The first sample was stored at -80°C as a backup. The second sample was processed for histology/pathology and HE or anti-M13 phage immunostaining. The third sample was divided under clean conditions to obtain three fragments with the same weight.
  • the triplicates from the third prostate sample were processed for host bacterial infection and phage recovery.
  • the prostate sample was transferred to 1 ml DMEM-protease inhibitors (PI) in a glass tissue grinder, homogenized and transfered cell suspension to an autoclaved 2 ml eppendorf tube.
  • PI DMEM-protease inhibitors
  • the prostate tissue samples were washed three times with ice cold DMEM-PI containing 1% BSA.
  • the tissue was mixed with DMEM-PI and vortexed for 30 seconds after each wash. After spinnig at 4,000 rpm for 3 min and the supernatant was carefully discarded (the tissue pellet should remain undisturbed).
  • 1.5 ml DMEM-PI/BSA was added.
  • the admixture was transferred to Falcon tubes containing 10 ml of LB medium plus 0.2 ⁇ g/ml of tetracycline at RT for 20 minute. Multiple aliquots were plated in LB tet/kan plates or dishes containing 40 ⁇ g/ml of tetracycline and 100 ⁇ g/ml kanamycin. Finally, dishes were incubated at 37°C and the phage transducing unit count determined after an overnight incubation.
  • Tumor blood vessels are known to be leaky. Longer term exposure of the mouse subject to a phage display library may result in migration of phage and binding to prostate cancer cell markers. Mice were incubated with a phage library for 24 hrs to target cancer cell markers.
  • mice Male nude mice (4 mice) were injected with 10 6 DU-145 cells in PBS. After tumor growth, the mice were injected with either a CX10C phage display library. After allowing the library to circulate for 24 hours, the mice were sacrificed and tissue samples were collected. Samples were homogenized in Dounce homogenizer and K91 bacteria were added to recover phage. Bacteria were plated on kan/tet LB plates in triplicate at a series of dilution. The remaing tumor homogenate with bacteria was incubated for 1 hr at RT with 10 ml of LB/tet/kan.
  • Prostate cancer targeting sequences identified by DNA sequencing the phage inserts are listed in Table 5. Table 5.
  • prostate targeting peptide sequences identified herein will be of use for numerous applications within the scope of the present invention, including but not limited to targeted delivery of therapeutic agents or gene therapy, in vivo imaging of normal or diseased organs, tissues or cell types, identification of receptors and receptor ligands in organs, tissues or cell types, and therapeutic treatment of a number of diseases, particularly prostate cancer.
  • Peptides homing to the mouse placenta were identified by a post-clearing protocol using a phage display library.
  • a first round of biopanning was performed on pregnant mice. Samples of placenta were removed and phage rescued according to the standard protocols described above, with one modification. In the typical bipanning protocol, thousands of phage may be recovered from a single organ, tissue or cell type. Typically, between 200 and 300 individual colonies were selected from plated phage and these were amplified and pooled to form the phage display library for the second or third rounds of biopanning.
  • phage were administered to a non-pregnant mouse. Phage that bound to tissues other than placenta were absorbed from the circulation. Remaining phage were recovered from the plasma of the non-pregnant mouse. This protocol was designed to isolate phage that bound to placenta but not to other mouse organs, tissues or cell types. The following placenta targeting peptides were identified, along with their frequencies. A search of the GenBank database disclosed that none of the SEQ ID NO's listed below was 100% homologous with any known peptide sequence.
  • TPKTSVT (SEQ ID NO:39) 7.4% in round III, 8.5% in round IV RMDGPVR (SEQ ID NO:40) 3.1% in round III, 8.5% in round IV RAPGGVR (SEQ ID NO:41) ⁇ 1% in round III, 8.5% in round IV VGLHARA (SEQ ID NO:42) 4.2% in round III, 7.4% in round IV YIRPFTL (SEQ ID NO:43) 2.1% in round III, 5.3% in round IV LGLRSVG (SEQ ID NO:44) ⁇ 1% in round III, 5.3% in round IV PSERSPS (SEQ ID NO:45) (data not available)
  • a post-clearing procedure resulted in a substantial enrichment of phage bearing placenta targeting peptides.
  • this procedure was used for placenta, the skilled artisan will realize that post-clearance can be performed on for any organ, tissue or cell type where a phage library can be administered to a subject lacking that organ, tissue or cell type.
  • a post-clearing procedure for prostate or testicle targeting peptides could be performed in a female subject, and for ovary, vagina or uterus in a male subject.
  • a homology search identified several candidate proteins as endogenous analogs of the placental targeting peptides, including TCR gamma-1 (TPKTSVT, SEQ ID NO:39), tenascin (RMDGPVR, SEQ ID NO:40 and RAPGGVR, SEQ ID NO:41), MHC Class II (LGLRSVG, SEQ ID NO:44), angiotensin I (YIRPFTL, SEQ ID NO:43) and MHC H2-D-q alpha chain (VGLHARA, SEQ ID NO:42).
  • TCR gamma-1 TPKTSVT, SEQ ID NO:39
  • tenascin RMDGPVR, SEQ ID NO:40 and RAPGGVR, SEQ ID NO:41
  • MHC Class II LGLRSVG, SEQ ID NO:44
  • angiotensin I YIRPFTL, SEQ ID NO:43
  • VGLHARA MHC H2-D-q alpha chain
  • FIG. 1 shows the results of the validation studies for selected placenta homing phage.
  • the phage clones are identified as: PA - TPKTSVT (SEQ ID NO:39), PC - RAPGGVR (SEQ ID NO:41), PE - LGLRSVG (SEQ ID NO:44), PF - YIRPFTL (SEQ ID NO:43). It can be seen that the PA clone exhibited placental homing more than an order of magnitude greater than observed with control fd-tet phage. The PC clone also showed substantially higher placental localization, while the PE and PF clones were not substantially enriched in placenta compared to control phage.
  • Table 6 shows the effects of the PA and PF placental targeting peptides injected into pregnant mice, attached to FITC (fluorescein isothiocyanate), GST (glutathion S-transferase) or to phage. At lower dosages (450 ⁇ g total), FITC conjugated PA and PF showed a slight effect on pregnancy (Table 6).
  • both protein and phage conjugated PA and PF peptides substantially interfered with fetal development (Table 6), apparently resulting in death of the fetuses in most cases.
  • the CARAC peptide (SEQ ID NO:46), an adipose targeting peptide (FE, TREVHRS, SEQ ID NO:47) or fd-tet phage were used as non-placental targeting controls. Table 6.
  • PA-FITC placenta homer
  • PF-FITC placenta homer
  • PF-FITC placenta homer
  • Avertin OD >death. fetuses-OK ?
  • fat targeting peptides from a genetically obese mouse (Zhang et al., 1994; Pelleymounter et al., 1995), with post-clearing performed in a normal mouse.
  • the fat-targeting peptides isolated included TRNTGNI (SEQ ID NO:48), FDGQDRS (SEQ ID NO:49); WGPKRL (SEQ ID NO:50); WGESRL (SEQ ID NO:51); VMGSVTG (SEQ ID NO:52), KGGRAKD (SEQ ID NO:53), RGEVLWS (SEQ ID NO:54), TREVHRS (SEQ ID NO:47) and HGQGVRP (SEQ ID NO:55).
  • the fat homing peptides were validated by in vivo homing, as shown in FIG. 2 .
  • the fat homing clones selected were: FA - KGGRAKD (SEQ ID NO:53), FC - RGEVLWS (SEQ ID NO:54), FE - TREVHRS (SEQ ID NO:47) and FX - VMGSVTG (SEQ ID NO:52).
  • FIG. 2 all of these clones exhibited some elevation of homing to adipose tissue, with clone FX showing several orders of magnitude higher adipose localization than control fd-tet phage.
  • targeting peptides selective for angiogenic vasculature in adipose tissue could be of use for weight reduction or for preventing weight gain.
  • anti-angiogenic or toxic moieties to an adipose targeting peptide, the blood vessels supplying new fat tissue could be selectively inhibited, preventing the growth of new deposits of fat and potentially killing existing fat deposits.
  • Mouse ovary targeting peptides include GLAKLIP (SEQ ID NO:56), HLISDMS (SEQ ID NO:57), LQHWLLS (SEQ ID NO:58), ALVLQG (SEQ ID NO:59).
  • TGVALQS SEQ ID NO:60
  • YVQSREG SEQ ID NO:61
  • PLFWPYS SEQ ID NO:62
  • DGSG SEQ ID NO:63
  • EGSG SEQ ID NO:64
  • SSPRPGV SEQ ID NO:65
  • DGYPAIA SEQ ID NO:66
  • GHAIE SEQ ID NO:67
  • IWSTSER SEQ ID NO:68
  • Targeting peptides against mouse ascites include YRLRG (SEQ ID NO:69), YRARG (SEQ ID NO:70), SQPLG (SEQ ID NO:71), SQPWG (SEQ ID NO:72), QRLVTP (SEQ ID NO:73), QVLVTP (SEQ ID NO:74), QRLVHP (SEQ ID NO:75), QVLVHP (SEQ ID NO:76), ITRWRYL (SEQ ID NO:77), SLGGMSG (SEQ ID NO:78), SQLAAG (SEQ ID NO:79), SLLAAG (SEQ ID NO:80), SQLVAG (SEQ ID NO:81), SLLAAG (SEQ ID NO:82), GLPSGLL (SEQ ID NO:83), HGGSANP (SEQ ID NO:84), SLEAFFL (SEQ ID NO:85), CVPELGHEC (SEQ ID NO:86), CELGFELGC (SEQ ID NO:87) AND CFFLRDWFC (SEQ ID NO:88).
  • Example 4 Screening an alpha-spleen antibody library in vivo by BRASIL
  • Targeting peptides against spleen have not been previously identified.
  • biopanning against spleen tissue is complicated by the high background of non-specific phage localization to spleen.
  • the decreased background observed in biopanning with the BRASIL method is advantageous for identifying targeting peptides against tissues such as spleen.
  • This example demonstrates an illustrative embodiment of the BRASIL method.
  • a phage library based on immunoglobulins derived against the target organ was developed and then subjected to in vivo biopanning.
  • mouse spleen was injected into a chicken. After boosting, the chicken spleen was collected and immunoglobulin variable domain sequences were obtained by PCRTM amplification of chicken spleen mRNA. The amplified immunoglobulin variable sequences were inserted into a phage display library ( ⁇ -library) that was then used for in vivo biopanning against mouse spleen.
  • ⁇ -library phage display library
  • the spleen targeting peptide sequences obtained from phage localized to mouse spleen in vivo were derived from antibody fragments produced in the chicken in response to mouse spleen antigens.
  • the success of this example further shows the broad utility of the BRASIL method. The skilled artisan will realize that the present invention is not limited to the embodiments disclosed herein and that many further developments of the BRASIL methodology are included in the scope of the present invention.
  • a white leghorn chicken was immunized with spleen homogenate (about 150 mg per injection) from a perfused (10 ml MEM) Balb/c mouse.
  • the chicken received spleen homogenate boosters at 4 weeks and 8 weeks after the initial immunization.
  • Immune response to mouse spleen by FACS analysis showed that the chicken immune serum contained antibodies against a mouse cell-line (TRAMP-C1).
  • the chicken was sacrificed and its spleen was removed to TRI Reagent (Molecular Research Center, Inc., Cincinatti, OH) 12 weeks after the first immunization.
  • RNA was prepared from the chicken spleen using the manufacturer's protocol for the TRI reagent.
  • cDNA was prepared from the total RNA using oligo(dT)-primers and Superscript enzyme (Life Technologies).
  • cDNAs encoding chicken spleen immunoglobulin variable regions were amplified by CHybVH and ChybIgB (V heavy ) or by CSCVK and CHHybL-B (V kappa ) primers according to standard techniques. Light chain variable regions and constant regions were PCRTM amplified together using CSC-F and lead-B primers and V kappa and C kappa templates.
  • Heavy chain variable regions and constant regions were PCRTM amplified together using dp-seq and lead-F primers and V heavy and C heavy templates. Heavy- and light -chain fragments were PCRTM amplified together with CSC-F and dp-Ex primers. PCR primers were purchased from Genosys or GenBase, using primer sequences listed in the Cold Spring Harbor laboratory course manual, "Phage Display of Combinatorial Antibody Libraries” (Barbas et al., 2000 ), the text of which is incorporated herein by reference.
  • mice Four rounds of in vivo screening in mice were performed using the chicken ⁇ -spleen library. About 0.8 to 2.0 x 10 10 TU were injected into a Balb/c mouse. The library was allowed to circulate for 5 minutes. After sacrifice, the mouse spleen was recovered and a single cell suspension was prepared by pressing the spleen through a 70 ⁇ m cell strainer nylon mesh. The single cell suspension was centrifuged over oil (9:1 dibutyl phtalate:cyclohexane) using the BRASIL technique and 200 ⁇ l of log phase ER2537 E. coli were infected with the pellet. Amplified phage recovered from the mouse spleen was used for the subsequent round of screening. No obvious enrichment in the screening rounds was seen in the number of phage homing to spleen and brain compared with the conventional biopanning method, using a piece of spleen obtained prior to BRASIL.
  • Phage locallized in mouse spleen from the fourth round of screening of the chicken Fab inserts were PCR TM amplified and the PCR product was digested with Bst I. Half of the clones out of 90 analyzed produced a similar restriction pattern. Of those, 20 clones were sequenced from which only two had an identical restriction pattern. Four of the antibody based phage clones (numbers 2, 6, 10 and 12) were subjected to further analysis using binding and localization assays.
  • a singe cell suspension was prepared from two mouse spleens. The suspension was divided into five tubes and incubated on ice with 3x10 9 TU of Fab clones #2, #6, #10, #12 and 2x10 9 TU tet-phage. Phage bound to mouse spleen cells were recovered by BRASIL. 200 ⁇ l of log phase ER2537 E.coli was infected with the pellet and serial dilutions were plated on LB/carbenicillin and LB/tetracyclin plates for assessment of phage binding. Fd-tet was used as an internal control to normalize all the phage homing experiments.
  • Phage (3x10 9 ) of Fab clones #2, #6, #10, #12 and 2x10 9 TU tet -phage were injected into the tail veins of Balb/c mice and allowed to circulate for 5 minutes. The spleens were recovered and single cell suspensions were prepared on ice from whole spleens. Cell bound phage were recovered by BRASIL. 200 ⁇ l of log phase ER2537 E.coli was infected with the pellet and serial dilutions were plated on LB/carbenicillin and LB/tetracycline plates for assessment of the phage recovery.
  • Phage (3x10 9 TU) of Fab clone #10 and NPC-3TT (control Fab phage) and 1x10 9 TU of control Fd-tet -phage were injected to mice (2 mice for NPC-3TT, 2 mice for clone #10) and allowed to circulate for 5 minutes. Spleens were recovered and single cell suspensions were prepared on ice. Cell-bound phage were recovered by BRASIL. 200 ⁇ l of log phase ER2537 E.coli was infected with the pellet and serial dilutions were plated on LB/carbenicillin and LB/tetracycline plates.
  • the NPC-3TT phage is a human anti-tetanus toxin Fab fragment displaying phage.
  • Phage (3x10 9 TU) of Fab clone #10 and NPC-3tt control and 1x10 9 TU of Fd-tet control phage were injected into mice (2 mice for NPC-3TT, 2 mice for clone #10) and allowed to circulate for 5 minutes. The spleens were recovered and single cell suspensions were prepared. Bone marrow was recovered from the same mice (both femurs) as a control for organ specific homing. Cell-bound phage were recovered by BRASIL.
  • the plasmid pComb3 containing the chicken Fab inserts was electroporated into ER2537 bacteria. Serial dilutions were plated onto LB/carbenicillin plates and incubated overnight at 37°C. Fab production culture (in super broth with 100 ⁇ g/ml carbenicillin) was started from a single plated colony. Fab production was induced with 1 mM IPTG for 7 hours at 30°C. The Fab fragment was purified from the periplasmic fraction SN2 by affinity purification after determination of the Fab concentration in bacteria supernatant, periplasmic fractions SN1 and SN2 and in the bacteria lysate by ELISA. An ⁇ -Fab-Protein G -column was coupled (2mg/ml) with dimethylpimelimidate (DMP) using standard protocols (Harlow and Lane, 1988).
  • DMP dimethylpimelimidate
  • the SN2 fraction was loaded into a 1 ml HiTrap-protein G- ⁇ -Fab-column (Amersham Pharmacia Biotech, Piscataway, NJ) either over 2 hours (if using lower than 50 ml volume with superloop) or overnight (with more than 50 ml volume using a peristaltic pump).
  • the column was washed with 10-20 ml of PBS (phosphate buffered saline).
  • the Fab fragments were eluted with 10 ml of 20 mM glycine buffer, pH 2.2, 150 mM NaCl and 1 ml fractions were collected. Fractions are neutralized with 1 M Tris immediately after elution. Protein concentrations were quantified by A 280 .
  • Fab#10, NPC3-tt or R#16 50 to 60 ⁇ g of Fab fragment (Fab#10, NPC3-tt or R#16) was injected into the tail vein of a Balb/c mouse and allowed to circulate for 8 minutes.
  • 50 ⁇ g of L.esculentum lectin-FITC was injected into the mouse and the mouse tissues were fixed by perfusion with 25 to 30 ml of 4% paraformaldehyde/PBS after 2 minutes of lectin circulation. Tissues were removed and post-fixed in 4% paraformaldehyde for 1 hour. Fixed tissues were incubated in 30% sucrose/PBS overnight at 4°C, changing the solution at least twice. The tissues were embedded in the freezing media and frozen on dry ice.
  • Fab clone #10 was selected for additional characterization by in vivo localization to mouse spleen.
  • the results, shown in FIG. 6 confirm that Fab clone #10 exhibted 3 to 10 fold enrichment in spleen compared to Fd-tet. This effect was not due to general Fab binding, since the Fab control phage NPC-3TT did not exhibit selective localization in spleen compared to Fd-tet insertless phage.
  • Binding of Fab clone #10 was organ specific, as demonstrated in FIG. 7 .
  • Phage from Fab clone #10 and NPC-3TT control were recovered from spleen and bone marrow tissue from the same injected mice. It can be seen in FIG. 7 that Fab clone #10 exhibited selective localization to spleen but not to bone marrow tissue. The control phage did not exhibit selective localization to bone marrow ( FIG. 7 ) or spleen (not shown).
  • Fab phage clone #10 selectively targets mouse spleen tissue for binding both in vitro and in vivo. These results were further validated by vascular staining for in vivo phage distribution. Control phage used for this study were clones NPC-3TT (Fab fragment) and clone R#16 (isolated from angiogenic retina screening).
  • Fab clone #10 was observed to bind to mouse spleen tissue in vivo by fluorescent staining (not shown).
  • the control phage NPC-3TT and R#16 did not stain spleen tissue under identical conditions.
  • the clone #10 and NPC-3TT phage were observed to intensively stain kidneys of injected animals, perhaps due to glomerular filtration (not shown).
  • Other control organs lung, brain, liver, heart and skeletal muscle did not show staining with clone #10 (not shown).
  • spleen targeting phage peptides can be identified by the BRASIL method. They further show the feasibility of the phage display technique using antibody fragments against a target organ, tissue or cell type to obtain a starting phage library. The ability to obtain targeting peptides against spleen, a tissue that has proven refractory to biopanning using standard phage display protocols because of the high non-specific background, shows the advantages of the BRASIL method.
  • Example 5 In vivo screening of ⁇ -Kaposi's sarcoma library in angiogenic retinas
  • An angiogenic retinal system has been developed as a model for angiogenic tumor tissues. Hypoxia in neonatal mice causes an angiogenic response in the retina. The angiogenic retinal tissue receptors show similarities with angiogenic tumor tissues in phage display binding.
  • mice One-week-old C57BL/6J mice were exposed to a 75% oxygen atmosphere for 5 days and then kept in room air for another five days.
  • the proliferative neovascular response was quantified by counting the nuclei of new vessels extending from the retina into the vitreous region in 6 ⁇ m cross-sections.
  • This model was used to assess binding to newly formed angiogenic vessels of a phage display library injected intravenously into mice. The peak of neovascularization was observed between postnatal days 17 to 21.
  • a Fab phage library ( ⁇ -KS) was produced against Karposi's sarcoma tumor tissue that had been immunized into a rabbit, using the same methods disclosed above for spleen. Three rounds of in vivo screening were performed using the ⁇ -KS library in the angiogenic retinal model system. About 3 to 10 x 10 10 TU of ⁇ -KS phage were injected into 2 C57BL/6 mice with hypoxia-induced retinal neaovascularization on postnatal days 18 to 20. The library was allowed to circulate for 5 minutes. Eyes were enucleated and retinas separated from the rest of the eye. A single cell suspension was prepared from the retinas by crushing them between two glass slides.
  • HUVEC cells were tested for their ability to bind to HUVEC cells.
  • Microtiter wells were coated with HUVECs in complete media. Cells were fixed and incubated overnight with supernatant from IPTG-induced cultures from phage infected bacteria. Fab production was detected by ⁇ -Fab ELISA. Fab binding to HUVECs was detected by ⁇ -Fab-AFOS ELISA.
  • FIG. 8 shows the results of Fab clone binding to HUVECs using an ⁇ -KS phage library. Clone #16 appeared to bind well to HUVECs in vitro .
  • Certain embodiments of the present invention concern the identification of receptor/ligand pairs for various applications.
  • Targeting peptides selective for organs, tissues or cell types bind to receptors (as defined above), normally located on the lumenal surface of blood vessels within the target.
  • targeting peptides may be used to identify or characterize such receptors, either directly or indirectly.
  • other therapeutic agents or imaging agents for in vivo imaging such naturally occuring receptors are of use as potential targets for development of new therapeutic agents directed against the receptor itself, for development of vaccines directed against the receptor, and for understanding the molecular mechanisms underlying various disease states.
  • the targeting peptides themselves may serve as the basis for new therapeutic agents directed against the receptors.
  • Targeting peptides may frequently act as mimeotopes of endogenous ligands that bind to the targeted receptor.
  • the endogenous ligands may be identified and characterized using the disclosed methods. Such ligands are also of potential use as targets for development of new therapeutic agents, etc.
  • the present example illustrates one embodiment related to identification of receptor/ligand pairs, in this case, integrin receptors.
  • integrin receptors Non-limiting examples of applications of targeting peptides directed against integrins include regulation of cell proliferation and chemotaxis, pro-apoptosis and anti-angiogenesis.
  • purified integrins attached to a solid substrate were used to screen phage display libraries to identify targeting peptides directed against integrins.
  • Integrin function is regulated by cytokines and other soluble factors in a variety of biological systems. Most commonly, exposure to such factors leads to conformational alterations that result in changes in the activation state of the receptors (i.e., increased or decreased affinity for a given ligand and/or receptor clustering in the plasma membrane). Changes in integrin-dependent adhesion ultimately activate various complex signal transduction pathways. At the molecular level, the induced colocalization of cytoskeleton proteins with integrin cytoplasmic domains controls signal transduction.
  • Cytoplasmic domains are key regulators of integrin function (reviewed in Hynes, 1992; Ruoslahti, 1996). Individual ⁇ and ⁇ subunit cytoplasmic domains are highly conserved among different species (Hemler et al., 1994). Although the cytoplasmic domains of various ⁇ subunits share similar primary structures, they differ in certain functional characteristics. Experiments with chimeric integrins have shown that the cytoplasmic domains of ⁇ chains are responsible for regulating receptor distribution and recruitment to focal adhesion sites (Pasqualini and Hemler, 1994). Thus, certain cytoplasmic domains are critical for integrin-mediated signaling into the cell (outside-in signaling) and activation of integrin-ligand binding activity (inside-out signaling) (Hemler et al., 1994).
  • integrins ⁇ v ⁇ 3 and ⁇ v ⁇ 5 are selectively expressed in angiogenic vasculature but not in normal vasculature (Brooks et al., 1994a, 1994b; Pasqualini et al., 1997; Arap et al ., 1998). Moreover, ⁇ v integrin antagonists have been shown to block the growth of neovessels (Brooks et al., 1994a, 1994b, 1995; Hammes et al ., 1996). In these experiments, endothelial cell apoptosis was identified as the mechanism for the inhibition of angiogenesis (Brooks et al ., 1994a, 1994b, 1995).
  • Angiogenesis initiated by bFGF can be inhibited by an anti- ⁇ v ⁇ 3 blocking antibody, whereas VEGF-mediated angiogenesis can be prevented by a blocking antibody against ⁇ v ⁇ 5.
  • the integrins ⁇ v ⁇ 3 and ⁇ v ⁇ 5 have been reported to be preferentially displayed in different types of ocular neovascular disease (Friedlander et al., 1995, 1996). Thus, distinct cytokine-induced pathways that lead to angiogenesis seem to depend on specific ⁇ v integrins.
  • ⁇ v ⁇ 3 and ⁇ v ⁇ 5 integrins bind to vitronectin, they probably mediate different post-ligand binding events. For instance, in the absence of exogenous soluble factors, the integrin ⁇ v ⁇ 5 fails to promote cell adhesion, spreading, migration, and angiogenesis. On the other hand, the ⁇ v ⁇ 3 integrin can induce such events without additional stimulation by cytokines (Klemke et al., 1994; Lewis et al ., 1996; Friedlander et al., 1995).
  • calphostin C an inhibitor of PKC
  • PKC activation probably affects the conformation or phosphorylation state of the ⁇ 5 cytoplasmic domain. Similar changes may occur in cytoplasmic proteins as well (Kolanus and Seed, 1997).
  • the cytokine regulation of ⁇ v ⁇ 5 integrin is unusual because ligand binding is unchanged, but the events that follow ligand binding differ (Lewis et al., 1996). Therefore, cellular events mediated by ⁇ v ⁇ 3 or ⁇ v ⁇ 5 are clearly controlled by different mechanisms (Filardo and Cheresh, 1994b).
  • ⁇ integrin cytoplasmic domains Several other proteins reportedly interact with ⁇ integrin cytoplasmic domains in general: talin, filamin, ⁇ -actinin, focal adhesion kinase, the serine/threonine kinase ILK, and skelemin. Talin, ⁇ -actinin, and focal adhesion kinase no longer co-localize with ⁇ 1 integrins after deletion of their putative binding sites in the ⁇ 1 cytoplasmic domain. Similar approaches have shown that other cytoskeleton-associated proteins and signaling molecules co-localize with integrins.
  • Integrins associate with molecules that are involved in growth factor signaling.
  • ⁇ v ⁇ 3 the 190-kDa protein and IRS-1, which can be found in association with ⁇ v ⁇ 3 (Vuori and Ruoslahti, 1994)
  • analysis of the association of the ⁇ v ⁇ 3 integrin with molecules related to the insulin and PDGF signaling pathways revealed that both the insulin and PDGFB receptors co-immunoprecipitate with ⁇ v ⁇ 3.
  • the receptor molecules associated with the integrin represent a highly phosphorylated and highly activated subfraction of such molecules. These results are important because they reinforce the notion that integrin-mediated cell attachment coordinates cellular responses to growth factors. Integrin-dependent signaling processes synergize with proliferation signals (Frisch and Ruoslahti, 1997; Clark and Brugge, 1995; Longhurst and Jennings, 1998).
  • Protein phosphorylation is one of the earliest events detected in response to integrin stimulation.
  • the ability of tyrosine kinase inhibitors to obstruct the formation of focal adhesions suggests a role for tyrosine phosphorylation in the signaling pathways linked to integrin receptors (Defilippi et al., 1994).
  • Serine/threonine kinase families such as protein kinase C (PKC) and mitogen-activated protein (MAP) kinase, are also activated upon integrin stimulation, and inhibitors of PKC block cell attachment and spreading in certain cell systems (Vuori and Ruoslahti, 1993).
  • Integrins seem to affect cell survival by regulating programmed cell death, a response that also depends on tyrosine phosphorylation.
  • Several proteins that associate with integrin protein complexes contain modular domains, termed Src homology 2 (SH2) and 3 (SH3), that specifically mediate protein-protein coupling.
  • SH2 domains bind to proteins through interactions with specific peptide motifs containing phosphotyrosine, whereas SH3 domains bind to short proline-rich peptide motifs on their protein targets (Clark and Brugge, 1995).
  • Integrin-mediated cell adhesion causes activation of MAP kinases and increased tyrosine phosphorylation of focal adhesion kinase (FAK).
  • FAK focal adhesion kinase
  • phage display technique offers an alternative approach to generating and selecting diverse combinatorial-peptide libraries (Smith, 1991; Wells and Lowman, 1992). Because the chemical diversity in a phage display library is encoded by DNA that can be replicated and amplified, selection of a phage library can be performed over multiple rounds, allowing even rare motifs to be identified. In contrast to synthetic chemical libraries, phage display permits the analysis of single species instead of pooled species. The power of this technique has been demonstrated mainly through the selection of rare antibodies or peptides from large combinatorial libraries.
  • a combinatorial phage library has been used for determining the preferred substrate sequences for different protein-tyrosine kinases (PTKs), all of them closely related members of the Src family and one more distantly related PTK, Syk (Schmitz et al., 1996). Subsequent phosphorylation by recombinant PTKs and selection of phosphorylated phage by an anti-phosphotyrosine antibody were used to enrich for phage that displayed substrate peptides. After several rounds of selection, distinct substrate sequences were found for each of the PTKs tested. For the PTKs related to the Src family, critical features of these canonical sequences were recapitulated in known or presumed protein substrates.
  • PTKs protein-tyrosine kinases
  • Phage were phosphorylated in vitro at an invariant tyrosine residue by a mixture of the phosphotyrosine kinases c-Src, Blk, and Syk. Binding motifs were selected by interaction of the library with the recombinant SH2 domain of Grb2 expressed as a glutathione-S-transferase (GST) fusion protein. Several subsequent cycles of selection led to the enrichment of phage that bound to the GST-Grb2 SH2 domain only when previously phosphorylated. Sequence analysis revealed that all of the selected phage displayed peptides with the consensus motif Y*M/NW (Y* denotes phosphotyrosine).
  • the cytoplasmic domain of ⁇ 5 is structurally and functionally unique with regard to other integrin subunits (Table 8) and shares only 38% homology to the cytoplasmic domain of ⁇ 3 (Hemler et al., 1994). It has been proposed that the structural requirements for association with ⁇ v prevented further primary sequence divergence between ⁇ 3 and ⁇ 5; yet the existing differences are likely to account for the reduced interaction of ⁇ v ⁇ 5 with talin (Lewis et al., 1996).
  • the cytoplasmic domain of ⁇ 5 when expressed in Chinese hamster ovary (CHO) cells as a chimera with the extracellular domain of ⁇ 1, led the chimeric receptor to behave like ⁇ 5, promoting cell migration and loss of receptor localization to focal adhesions (Pasqualini and Hemler, 1994).
  • the cytoplasmic domains of integrin ⁇ 1 and ⁇ 3 subunits were shown to be functionally interchangeable (Solowska et al., 1991).
  • Other studies have shown that ⁇ v ⁇ 3 and ⁇ v ⁇ 5 seem to differ in terms of localization to focal adhesion and their contribution to cell migration (Delannet et al., 1994; Filardo et al., 1995).
  • ⁇ v cytoplasmic domain may also be possible, in the context of each of the heterodimers. For example, a ⁇ turn in the cytoplasmic tail of the integrin ⁇ v subunit has been shown to influence conformation and ligand binding of ⁇ v ⁇ 3 (Filardo and Cheresh, 1994).
  • the basis of selective signaling properties may be the assembly of specific molecules that associate with the respective cytoplasmic domains.
  • the present study defines the molecules involved in ⁇ v ⁇ 3- and ⁇ v ⁇ 5-selective angiogenic signaling by exploring a novel strategy, panning of phage display peptide libraries on ⁇ 3 and ⁇ 5 cytoplasmic domains and determining the biological properties of the cytoplasmic domain-binding peptides.
  • the disclosed methods have several advantages over previous approaches: (i) the ability to characterize the intracellular molecules that directly or indirectly interact with integrin cytoplasmic domains; (ii) the development of antibodies against molecules that bind to integrin cytoplasmic domains in very low amounts; and (iii) the phage display library screenings will lead to the identification of peptides that mimic cytoplasmic-domain binding proteins.
  • KS1767 cells Herndier et al., 1996), HUVECs (ATCC), and BCE cells (Solowska et al., 1991).
  • Sterile glass coverslips covered with different proteins i.e. vitronectin, fibronectin, collagen, or laminin
  • the monolayers were rendered quiescent by a 12-hour incubation in medium containing 0.05% fetal calf serum.
  • Peptides were introduced into the cells using the penetratin membrane-permeable tag (see below).
  • the cells were plated onto ECM proteins for adhesion and spreading.
  • the monolayer was stimulated for 6 hours with each of the growth factors involved in ⁇ v-mediated angiogenesis, including bFGF, TNF ⁇ , VEGF, and TGF ⁇ . Untreated cells were the negative controls.
  • Cell migration assays were performed as follows: 48-well microchemotaxis chambers were used. Polyvinylpyrrolidone-free polycarbonate filters (Nucleopore, Cambridge, MA) with 8- ⁇ m pores were coated with 1% gelatin for 10 min at room temperature and equilibrated in M199 medium supplemented with 2% FCS. Peptides were placed in the lower compartment of a Boyden chamber in M199 supplemented with 2% FCS, 20 ng/ml VEGF-A (R&D System), and 1 U/ml heparin. Overnight-starved subconfluent cultures were quickly trypsinized, and resuspended in M199 containing 2% FCS at a final concentration of 2 ⁇ 10 6 cells/ml.
  • Apoptosis Assay (propidium iodide staining subdiploid population)
  • Angiogenic factors and tumor cells implanted into CAM stimulate growth of new capillaries.
  • Angiogenesis was induced in CAMs from 10-day chicken embryos by VEGF or bFGF filters implanted in regions that were previously avascular.
  • Different treatments penetratin peptides and controls
  • the number of blood vessels entering the disk was quantified within the focal plane of the CAM with a stereomicroscope. The mean number of vessels and standard errors from 8 CAMs in each group were compared.
  • Purified phage (10 ⁇ l) were incubated for 3 hours at room temperature with different concentrations (35 to 3,500 units) of protein kinases in a reaction buffer volume of 50 ⁇ l.
  • the reaction mixtures were transferred to tubes containing 10 ⁇ g of agarose-conjugated anti-P-Tyr, anti-P-Ser, or anti-P-Thr monoclonal antibodies to select phage displaying phosphorylated peptides.
  • Bound phage were eluted by washing the column with 0.3 ml of elution buffer (0.1 M NaCl/glycine/1 mg/ml BSA, pH 2.35).
  • the eluates were neutralized with 2 M Tris-base and incubated with 2 ml of a mid-log bacteria culture. Aliquots of 20 ⁇ l were removed for plating, and phage were harvested as described. The phosphorylation-selection step was repeated. Phosphorylated peptides binding to ⁇ 3 and ⁇ 5 cytoplasmic domains were analyzed as described in the previous section.
  • Matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry was used to map in vitro phosphorylation sites on the ⁇ 3 and ⁇ 5 cytoplasmic domains and cytoplasmic domain-binding peptides.
  • the fusion proteins or peptides were phosphorylated in vitro as described and purified by RP-HPLC or RP microtip columns.
  • Phosphorylated peptides were identified by three methods: (1) 80-Da mass shifts after kinase reactions; (2) loss of 80 Da after phosphatase treatment; or (3) loss of 80 Da or 98 Da in reflector vs.
  • peptides were purified by RP-HPLC and subjected to carboxypeptidase and aminopeptidase digestions to produce sequence ladders. This was particularly useful where one peptide may harbor two or more phosphorylation sites.
  • GST fusion proteins were phosphorylated in vitro as described (Schmitz et al., 1996; Dente et al., 1997; Gram et al., 1997). Briefly, 10 ⁇ g/ml was incubated for 3 h at room temperature with 5.5 units of Fyn protein kinase in reaction buffer (50 mM Tris, 5mM MgCl 2 , 500 ⁇ M Na 3 VO 4 , 500 ⁇ M ATP in a total volume of 50 ⁇ l). The reaction was stopped by adding 40% of TCA. After the kinase substrate protein was precipitated, it was resuspended in PBS and coated on microtiter wells at 10 ⁇ g/well. An aliquot of CX7C library (2.5x10 11 transducing units was incubated on the GST fusion proteins. Phage were sequenced from randomly selected clones.
  • Mass spectrometric peptide mass mapping was used to identify novel ligands for ⁇ 3 and/or ⁇ 5 cytoplasmic domains.
  • Polyclonal and monoclonal antibodies raised against the cytoplasmic domain-binding peptides were used to purify target proteins (cytoskeletal or signaling molecules). These proteins were resolved by SDS-PAGE, cut out from the SDS gels, and digested in-gel with trypsin. After extraction of the peptides, MALDI-TOF mass spectrometry analysis was performed to produce a list of peptide masses. This list of peptide masses, in combination with protease specificity, produces a relatively specific "signature" that can be used to search sequence databases. If the protein sequence is present in a database, the protein can be identified with high confidence by this method. The lower detection limit for this approach is currently 1 pmol, at least 10-20- fold better than N-terminal Edman sequencing methods.
  • ⁇ 3 and ⁇ 5 cytoplasmic domain-binding peptides were isolated by screening multiple phage libraries with recombinant GST fusion proteins that contained either GST- ⁇ 3cyto or GST- ⁇ 5cyto coated onto microtiter wells. Immobilized GST was used as a negative control for enrichment during the panning of each cytoplasmic domain. Phage were sequenced from randomly selected clones after three rounds of panning as disclosed elsewhere (Koivunen et al ., 1995; Pasqualini et al ., 1995). Distinct sequences were isolated that interacted specifically with the ⁇ 3 or with the ⁇ 5 cytoplasmic domains (Table 9). Randomly selected clones from panning rounds II and III were sequenced.
  • FIG. 9 shows the results from binding assays performed with the GST- ⁇ 3cyto binding phage. Six phage were tested that displayed the motifs most frequently found during the second and third rounds of panning. Each panel shows the results from binding assays for the phage displaying different peptides that bind to the ⁇ 3 cytoplasmic domain, as indicated. Insertless phage or unselected libraries were used as negative controls and did not show binding above background. Two plating dilutions were shown for each assay.
  • the binding assays were performed with individually amplified phage, shown in FIG. 10 . Five phage were tested that displayed the motifs found most frequently during the second and third rounds of panning. Each panel shows the binding assays for the phage displaying peptides that bind to the ⁇ 5 cytoplasmic domain. Insertless phage or unselected libraries were used as negative controls and did not show binding above background in these assays.
  • binding assays were performed comparing the interaction of individual phage motifs with ⁇ 1, ⁇ 3, or ⁇ 5 cytoplasmic domain fusion proteins.
  • ELISA with anti-GST antibodies showed that the three proteins can be coated onto plastic at equivalent efficiency, and thus the differences in binding do not reflect differences in coating concentrations (not shown).
  • the average selectivity for integrin cytoplasmic domains versus BSA was about one to two orders of magnitude (not shown). None of the phage tested seemed to bind strongly to the ⁇ 1 cytoplasmic domain (not shown).
  • Phosphorylation events modulate the interaction of the selected peptides with cytoplasmic domains
  • the phage display system was used to evaluate the effect of tyrosine phosphorylation at two levels. First, recombinant fusion proteins containing ⁇ 3 or ⁇ 5 cytoplasmic domains were used for panning of phage libraries displaying tyrosine-containing peptides. Second, the cytoplasmic domains themselves were phosphorylated before phage selection was performed. Experiments were performed to investigate the capacity of specific tyrosine kinases to modulate the interaction of the selected peptides with the cytoplasmic domains. The results obtained in the panning of phage libraries displaying tyrosine-containing peptides are shown in Table 10.
  • Randomly selected clones from rounds III and IV were sequenced from a X4YX4 phosphorylated library with Fyn. Amino acid sequences of the phagemid encoded peptides were deduced from nucleotide sequences. Table 10 shows the motifs found most frequently after the indicated libraries were panned with ⁇ 3 or ⁇ 5. The ratio of binding to ⁇ 3 or ⁇ 5 was calculated by dividing the number of ⁇ 3 or ⁇ 5 colonies by GST or BSA colonies found after panning. The ratio of binding to ⁇ 3 or ⁇ 5 with phosphorylated phage by Fyn versus unphosphorylated phage was calculated by dividing the number of colonies found after the panning. Table 10.
  • Phage displaying the ⁇ 3 and ⁇ 5 cytoplasmic domain-binding peptides were phosphorylated in vitro as previously described (Schmitz et al., 1996; Dente et al., 1997; Gram et al., 1997), using Fyn kinase.
  • Specific phosphorylation of the tyrosine-containing peptide on the surface of the phage was confirmed by using 32 P-gamma dATP in the kinase reaction and by separating the phage pIII protein by SDS-PAGE.
  • Phage phosphorylated in vitro showed increased binding affinity and specificity to the ⁇ 3 integrin cytoplasmic domain ( FIG. 13 ).
  • the TLRKYFHSS (SEQ ID NO:120) phage was also tested in assays that included other GST-cytoplasmic domain fusion proteins to determine specificity ( FIG. 14 ).
  • the peptides displayed by integrin cytoplasmic domain-binding phage were similar to certain regions found within cytoskeletal proteins and proteins involved in signal transduction (Table 11).
  • the similarity of some of the isolated peptides to a region of mitogen-activated protein kinase 5 (MAPK5, amino acids 227-234) was particularly interesting.
  • a connection involving the MAPK cascade, cell adhesion, migration and proliferation has been proposed (Lin et al., 1997) Table 11. Sequence similarity of integrin binding peptides with known cytoskeletal and signaling proteins.
  • Penetratin is a peptide that can translocate hydrophilic compounds across the plasma membrane. Fusion to the penetrating moiety allows oligopeptides to be targeted directly to the cytoplasm, nucleus, or both without apparent degradation (Derossi et al., 1994).
  • This membrane-permeable peptide consists of 16 residues (RQIKIWFQNRRMKWKK, SEQ ID NO:122) corresponding to amino acids 43-58 of the homeodomain of Antennapedia, a Drosophila transcription factor (Joliet et al., 1991a, 1991b; Le Roux et al., 1993). Internalization mediated by penetratin occurs at both 37°C and 4°C, and the internalized peptide can be retrieved intact from cells.
  • Peptides were designed containing penetratin sequences fused to the sequences of motifs found to bind ⁇ 3 or ⁇ 5 cytoplasmic domains.
  • the peptides were synthesized on a 431 Applied Biosystems peptide synthesizer using p-hydroxymethylphenoxy methyl polystyrene (HMP) resin and standard Fmoc chemistry. Peptide internalization and visualization was performed as described (Derossi et al., 1994; Hall et al., 1996; Theodore et al., 1995).
  • cytoplasmic domain-binding peptides selected on ⁇ 3 or ⁇ 5 can interfere with integrin-mediated signaling and subsequent cellular responses (i.e., endothelial cell adhesion, spreading, proliferation, migration).
  • integrin-mediated signaling i.e., endothelial cell adhesion, spreading, proliferation, migration.
  • SDNRYIGSW SEQ ID NO:97
  • CEQRQTQEGC SEQ ID NO:93
  • ⁇ 3 binding peptides and VVISYSMPD SEQ ID NO:112; a ⁇ 5-binding peptide
  • These complex chimeric peptides consist of the most selective of the ⁇ 3 or ⁇ 5-cytoplasmic domain-binding peptides coupled to penetratin, plus a biotin moiety to allow the peptides to be tracked once they were internalized into intact cells.
  • FIG. 15 The effect of ⁇ 3 and ⁇ 5 integrin cytoplasmic domain-binding motifs on endothelial cell proliferation was evaluated after stimulation with factors that activate endothelial cells ( FIG. 15 ).
  • Cell proliferation was measured according to Pasqualini and Hemler (1994). Briefly, 4x10 4 HUVECs were incubated in 24-well plates and starved for 24 h, after which the medium was removed and replaced in the presence of VEGF and 15 ⁇ M of each peptide. After another 18 h of incubation, 50 ⁇ l of medium containing [ 3 H]thymidine (1 ⁇ Ci/ml) was added to the wells.
  • ⁇ 3 and ⁇ 5 integrin cytoplasmic domain-binding motifs were evaluated after stimulation with factors that activate endothelial cells.
  • the peptides tested affected cell function in a dose-dependent and specific way. Their properties seem to be intrinsic to the ⁇ 3 or to the ⁇ 5 cytoplasmic domain ( FIG. 16 ).
  • Apoptosis assay Propidium Iodide (PI) staining subdiploid population.
  • XL Coulter Coulter Corporation
  • Polyclonal antibodies that recognize ⁇ v ⁇ 3 and ⁇ v ⁇ 5-binding peptides were generated using KLH conjugates made with the synthetic peptides, according to standard techniques. Antibodies against two different synthetic peptides have been produced ( FIG. 18 ). The sera not only recognize the immobilized peptides, but also recognize specific proteins in total cell extracts, as shown by western blot analysis ( FIG. 19 ).
  • Rabbits were immunized with SDNRYIGSW (SEQ ID NO:97) or GLDTYRGSP (SEQ ID NO:96) -KLH conjugates. Each rabbit was injected with 200 ⁇ g of peptide conjugated with KLH in Complete Freund's Adjuvant. Between 20 and 60 days later, the rabbits were injected with 100 ⁇ g Incomplete Freund's Adjuvant. After the third immunization, sera was collected. Preimmune serum obtained before the first immunization was used as an additional control in the experiments.
  • the polyclonal antibodies were tested by ELISA, Western blot and immunoprecipitation.
  • ELISA assays microtiter well plates were coated with 10 ⁇ g/ml of peptides. The plates were dried at 37°C, blocked with PBS+3% BSA, and incubated with different serum dilutions in PBS+1% BSA. After washing and incubation with the secondary antibody, an alkaline phosphate substrate was added and antibody binding detected colorimetrically at 405 nm. The reactivity observed both in the mouse and rabbit polyclonal sera was highly specific.
  • targeting peptides against specific domains of cell receptors can be identified by phage display.
  • Such peptides may be used to identify the endogenous ligands for cell receptors, such as endostatin.
  • the peptides themselves may have therapeutic effects, or may serve as the basis for identification of more effective therapeutic agents.
  • the endostatin targeting peptides identified herein when introduced into cells, showed effects on cell proliferation, chemotaxis and apoptosis.
  • the skilled artisan will realize that the present invention is not limited to the disclosed peptides or therapeutic effects.
  • Other cell receptors and ligands, as well as inhibitors or activators thereof, may be identified by the disclosed methods.
  • Example 9 showed that the VISY peptide (VVISYSMPD, SEQ ID NO:112), imported into cells by attachment to penetratin, could induce apoptosis in HUVEC cells.
  • Antibodies raised against the VISY peptide were used to identify the endogenous cell analog of the peptide, identified herein as Annexin V.
  • Annexin V is an endogenous ligand for the integrins that is involved in a novel pathway for apoptosis.
  • VVISYSMPD Polyclonal antibodies against the VISY peptide (VVISYSMPD, SEQ ID NO:112) were prepared using the methods described in Example 9 above.
  • MDA-MB-435 breast carcinoma cells were used for purification of the endogenous VISY peptide analog.
  • Cells were washed three times with ice cold PBS and lysed with chilled water for 20 mn.
  • Cell extracts were centrifuged for 30 min at 100,000 x g to separate the cytoplasmic fraction from the membrane fraction.
  • the cytoplasmic fraction was subjected to column chromatography on a gel filtration column (10-50kDa) and an anion exchange column (mono Q).
  • the anion exchange column was eluted with a salt gradient from 50 mM to 1 M NaCl.
  • fractions were collected, run on SDS-PAGE and tested by Western blotting for the presence of endogenous proteins reactivce with the anti-VISY antibody.
  • the fraction of interest containing a 36 kDa antibody reactive band, eluted at about 300 mM NaCl.
  • the 36 kDa always appeared in fractions that showed positive reactivity with the anti-VISY antibody.
  • the fractions were analyzed by SDS-PAGE and 2-D gel electrophoresis, followed by Western blotting. A substantial enrichment of the 36 kDa protein was seen after column chromatography (not shown).
  • the 36 kDa peptide was cut from the SDS-PAGE gel and analyzed by mass spectroscopy to obtain its sequence. All five peptide sequences that were obtained by mass spectroscopy showed 100% homology to the reported sequence of Annexin V (GenBank Accession No. GI_468888). In addition to its presnece in 435 cells, the 36 kDa band was also seen in Kaposi sarcoma, SKOV and HUVEC cells (not shown).
  • FIG. 20A shows the relative levels of binding of anti-Annexin V antibody to purified Annexin V and to VISY peptide.
  • Penetratin peptide chimera binding to the ⁇ 5 cytoplasmic domain induces programmed cell death.
  • Example 9 The induction of apoptosis by VISY peptide was shown in Example 9 was confirmed. 10 6 HUVEC were treated with 15 ⁇ M of VISY antennapedia (penetratin) chimera or 15 ⁇ M of antennapedia peptide (pentratin) alone for 2-4 hours and chromatin fragmentation was analyzed by electrophoresis in an agarose gel.
  • FIG. 21 shows the induction of apoptosis by VISY-Ant (penetratin), as indicated by chromatin fragmentation. Neither VISY or penetratin alone induced apoptosis.
  • VISY peptide A distinction between the mechanism of cell death induced by VISY peptide and other pro-apoptosis agents is that other apoptotic mechanisms evaluated in cell culture typically involve detachment of the cells from the substrate, followed by cell death. In contrast, in VISY induced cell death, the cells do not detach from the substrate before dying. Thus, endothanos (death from inside) appears to differ from anoikis (homelessness).
  • Example 9 and the present results show that VISY peptides activate an integrin dependent apoptosis pathway.
  • the present example shows that the endogenous analog for VISY peptide in Annexin V.
  • These results demonstrate the existence of a novel apoptotic pathway, mediated through an interaction between Annexin V and ⁇ 5 integrin and dependent on caspase activity. This novel apoptotic mechanism is termed endothanos.
  • the skilled artisan will realize that the existence of a novel mechanism for inducing or inhibiting apoptosis is of use for a variety of applications, such as cancer therapy.
  • Endothelial cells in tumor vessels express specific angiogenic markers.
  • Aminopeptidase A (APA, EC 3.4.11.7) is upregulated in microvessels undergoing angiogenesis.
  • APA is a homodimeric, membrane-bound zinc metallopeptidase that hydrolyzes N-terminal glutamyl or aspartyl residues from oligopeptides (Nanus et al ., 1993).
  • APA converts angiotensin II to angiotensin III.
  • the renin-angiotensin system plays an important role in regulating several endocrine, cardiovascular, and behavioral functions (Ardaillou, 1997; Stroth and Unger, 1999). Recent studies also suggest a role for angiotensins in angiogenesis (Andrade et al ., 1996), but the function of APA in the angiogenic process has not been investigated so far.
  • targeting peptides capable of binding APA were identified by screening phage libraries on APA-expressing cells.
  • Soluble CPRECESIC (SEQ ID NO:123) peptide inhibited migration, proliferation, and morphogenesis of endothelial cells in vitro and interfered with in vivo angiogenesis in a chick embryo chorioallantoic membrane (CAM) assay.
  • CAM chick embryo chorioallantoic membrane
  • APA null mice had a decreased amount of retinal neovascularization compared to wild type (wt) mice in hypoxia-induced retinopathy in premature mice.
  • the renal carcinoma cell line SK-RC-49 was transfected with an expression vector encoding full-length APA cDNA (Geng et al ., 1998).
  • Cells were maintained in MEM (Irvine Scientific, Santa Ana, CA), supplemented with 2 mM glutamine, 1% nonessential amino acids, 1% vitamins (Gibco BRL), 100 U/ml streptomycin, 100 U/ml penicillin (Irvine Scientific), 10 mM sodium pyruvate (Sigma-Aldrich), and 10% fetal calf serum (FCS) (Tissue Culture Biological, Tulare, CA). Stably transfected cells were maintained in G418-containing medium.
  • HUVECs were isolated by collagenase treatment and used between passages 1 to 4.
  • Cells were grown on gelatin-coated plastic in M199 medium (Sigma) supplemented with 20% FCS, penicillin (100 U/ml), streptomycin (50 ⁇ g/ml), heparin (50 ⁇ g/ml), and bovine brain extract (100 ⁇ g/ml). All media supplements were obtained commercially (Life Technologies, Inc., Milan, Italy).
  • the anti-APA mAb RC38 (Schlingemann et al ., 1996) was used to immunocapture APA from transfected cell lysates.
  • CPRECESIC SEQ ID NO:123
  • GACVRLSACGA SEQ ID NO:124
  • cyclic peptides were chemically synthesized, spontaneously cyclized in non-reducing conditions, and purified by mass spectrometry (AnaSpec San Jose, CA).
  • the mass spectrometer analysis of the CPRECESIC (SEQ ID NO:123) peptide revealed six different peaks, possibly reflecting different positions of disulfide bounds and the formation of dimers. Due to the similar biochemical behavior of the different fractions on APA enzyme activity, a mix of the six peaks was used in all procedures described below.
  • Microtiter round-bottom wells (Falcon) were coated with 2 ⁇ g of RC38 for 4 h at room temperature and blocked with PBS/3% BSA (Intergen, Purchase, NY) for 1 h at room temperature, after which 150 ⁇ l of cell lysate (1 mg/ml) was incubated on the mAb-coated wells overnight at 4°C, washed five times with PBS/0.1% Tween-20 (Sigma), and washed twice with PBS.
  • PBS/3% BSA Intergen, Purchase, NY
  • a CX 3 CX 3 CX 3 C (C, cysteine; X, any amino acid) library was prepared (Rajotte et al ., 1998). Amplification and purification of phage particles and DNA sequencing of phage-displayed inserts were performed as described above. Cells were detached by incubation with 2.5 mM EDTA in PBS, washed once in binding medium (DMEM high glucose supplemented with 20 mM HEPES and 2% FCS), and resuspended in the same medium at a concentration of 2x10 6 cells/ml.
  • binding medium DMEM high glucose supplemented with 20 mM HEPES and 2% FCS
  • the cell binding assay was performed with an input of 10 9 TU as described for the cell panning. The specificity was confirmed by adding CPRECESIC (SEQ ID NO:123) peptide to the binding medium in increasing concentrations.
  • CPRECESIC SEQ ID NO:123
  • phage binding on immunocaptured APA wells were blocked for 1 h at room temperature with PBS/3% BSA and incubated with 10 9 TU for 1 h at room temperature in 50 ⁇ l PBS/3% BSA. After eight washes in PBS/1% BSA/0.01% Tween-20 and two washes in PBS, phage were rescued by adding 200 ⁇ l of exponentially growing K91Kan E. coli. Each experiment was repeated at least three times.
  • MDA-MB-435-derived tumor xenografts were established in female nude mice 2 months old (Jackson Labs, Bar Harbor, Maine). Mice were anesthetized with Avertin and injected intravenously through the tail vein with 10 9 TU of the phage in a 200 ⁇ l volume of DMEM. The phage were allowed to circulate for 5 min, and the animals were perfused through the heart with 5 ml of DMEM. The tumor and brain were dissected from each mouse, weighed, and equal amounts of tissue were homogenized. The tissue homogenates were washed three times with ice-cold DMEM containing a proteinase inhibitor cocktail and 0.1% BSA.
  • Bound phage were rescued and counted as described for cell panning. Fd-tet phage was injected at the same input as a control. The experiment was repeated twice. In parallel, part of the same tissue samples were fixed in Bouin solution, and imbedded in paraffin for preparation of tissue sections. An antibody to M-13 phage (Amersham-Pharmacia) was used for the staining.
  • HUVECs were seeded in 48-well plates (10 4 cells/well) and allowed to attach for 24 h in complete M199 medium. The cells were then starved in M199 medium containing 2% FCS for 24 h.
  • CPRECESIC SEQ ID NO:123
  • control GACVRLSACGA SEQ ID NO:124
  • VEGF-A R&D System, Abingdom, UK
  • cells were fixed in 2.5% glutaraldehyde, stained with 0.1% crystal violet in 20% methanol, and solubilized in 10% acetic acid. All treatments were done in triplicate. Cell growth was evaluated by measuring the O.D. at 590 nm in a microplate reader (Biorad, Hercules, CA). A calibration curve was established and a linear correlation between O.D. and cell counts was observed between 10 3 and 10 5 cells.
  • a cell migration assay was performed in a 48-well microchemotaxis chamber (NeuroProbe, Gaithersburg, MD) according to Bussolini et al . (1995).
  • Polyvinylpyrrolidone-free polycarbonate filters (Nucleopore, Cambridge, MA) with 8- ⁇ m pores were coated with 1% gelatin for 10 min at room temperature and equilibrated in M199 medium supplemented with 2% FCS.
  • CPRECESIC SEQ ID NO:123
  • control GACVRLSACGA SEQ ID NO:124 peptide (1 mM) was placed in the lower compartment of a Boyden chamber in M199 medium supplemented with 2% FCS and 10 ng/ml VEGF-A (R&D System).
  • Subconfluent cultures that had been starved overnight were harvested in PBS containing 2.5 mM EDTA, washed once in PBS, and resuspended in M199 medium containing 2% FCS at a final concentration of 2 ⁇ 10 6 cells/ml. After the filter was placed between the lower and upper chambers, 50 ⁇ l of the cell suspension was seeded in the upper compartment, and cells were allowed to migrate for 5 h at 37°C in a humidified atmosphere with 5% CO 2 . The filter was then removed, and cells on the upper side were scraped with a rubber policeman. Migrated cells were fixed in methanol and stained with Giemsa solution (Diff-Quick, Baxter Diagnostics, Rome, Italy). Five random high-power fields (magnitude 100 ⁇ ) were counted in each well. Each assay was run in triplicate.
  • Matrigel (Collaborative Research, Bedford, MA) was added at 100 ⁇ l per well to 48-well tissue culture plates and allowed to solidify for 10 min at 37°C. HUVECs were starved for 24 h in M199 medium supplemented with 2% FCS before being harvested in PBS containing 2.5 mM EDTA. 10 4 cells were gently added to each of the triplicate wells and allowed to adhere to the gel coating for 30 min at 37°C. Then, medium was replaced with indicated concentrations of CPRECESIC (SEQ ID NO:123) or GACVRLSACGA (SEQ ID NO:124) peptides in complete medium. The plates were photographed after 24 h with an inverted microscope (Canon). The assay was repeated three times.
  • mice have been described (Lin et al ., 1998). Mice pups on P7 (7 th day post-partum) with their nursing mothers were exposed to 75% oxygen for 5 days. Mice were brought back to normal oxygen (room air) on P12. For histological analysis mice were killed between P17 and P21 and eyes were enucleated and fixed in 4% paraformaldehyde in PBS overnight at +4°C. Fixed eyes were imbedded in paraffin and 5 ⁇ m serial sections were cut. Sections were stained with hematoxylin/eosin (h/e) solution. Neovascular nuclei on the vitreous side of the internal limiting membrane were counted from 20 h/e-stained sections per each eye. The average number of neovascular nuclei per section was calculated and compared between animal groups using Student's t-test.
  • SK-RC-49 renal carcinoma cells which do not express APA, were transfected with full-length APA cDNA to obtain a model of APA expression in the native conformation.
  • APA expressed as a result of transfection was functionally active, as evidenced by an APA enzyme assay (not shown), but parental SK-RC-49 cells showed neither APA expression nor activity (not shown).
  • the CX 3 CX 3 CX 3 CX 3 C phage library (10 10 transducing units [TU]) was preadsorbed on parental SK-RC-49 cells to decrease nonspecific binding. Resuspended SK-RC-49/APA cells were screened with phage that did not bind to the parent cells. SK-RC-49/APA-bound phage were amplified and used for two consecutive rounds of selection. An increase in phage binding to SK-RC-49/APA cells relative to phage binding to SK-RC-49 parental cells was observed in the second and third rounds (not shown).
  • Selected phage inserts are specific APA ligands.
  • Phage displaying the peptide inserts CYNLCI RECESIC GADGACWTWCADGCSRSC (SEQ ID NO:125), CPKV CPRECES NC (SEQ ID NO:127) or CLGQCA SIC VNDC (SEQ ID NO:126) were individually tested for APA binding. All three phage specifically bound to the surface of SK-RC-49/APA cells (not shown), with a similar pattern of 6-fold enrichment relative to SK-RC-49 parental cells. Control, insertless phage showed no binding preference (not shown).
  • CGTGCAV ECE VVC (SEQ ID NO:128) and the other phage selected in round 2 showed no selective binding to SK-RC-49/APA cells (data not shown).
  • a soluble peptide, CPRECESIC SEQ ID NO:123 containing a consensus sequence reproducing the APA-binding phage inserts was synthesized.
  • Binding assays were performed with CPKV CPRE CESNC (SEQ ID NO:127) phage in the presence of the CPRECESIC (SEQ ID NO:123) peptide. Soluble CPRECESIC (SEQ ID NO:123) peptide competed with CPKV CPRE CESNC (SEQ ID NO:127) phage for binding to SK-RC-49/APA cells, but had no effect on nonspecific binding to SK-RC-49 parental cells (not shown. The unrelated cyclic peptide GACVRLSACGA (SEQ ID NO:124) had no competitive activity (not shown).
  • APA was partially purified from APA-transfected cell extracts by immunocapture with mAb RC38.
  • the APA protein immobilized on RC38-coated microwells was functional, as confirmed by enzyme assay (not shown).
  • the CYNL CIRECESI CGADGACWTWCADGCSRSC (SEQ ID NO:125), CPKV CPRECE SNC (SEQ ID NO:127), and CLGQCASICVNDC (SEQ ID NO:126) phage selectively bound immunocaptured APA, with a 10- to 12-fold enrichment compared to phage binding to RC38-immunocaptured cell lysates from SK-RC-49 parental cells (not shown).
  • CPKVCPRECESNC SEQ ID NO:127
  • CPRECESIC (SEQ ID NO:123) is a specific inhibitor of APA activity.
  • CPRECESIC SEQ ID NO:123
  • SK-RC-49/APA cells were incubated with the APA specific substrate ⁇ -glutamyl-p-nitroanilide in the presence of increasing concentrations of either CPRECESIC (SEQ ID NO:123) or control GACVRLSACGA (SEQ ID NO:124) peptides.
  • Enzyme activity was evaluated by a colorimetric assay after 2 h incubation at 37°C.
  • CPRECESIC SEQ ID NO:123
  • CPRECESIC (SEQ ID NO:123) for enzyme inhibition was calculated to be 800 ⁇ M.
  • CPRECESIC (SEQ ID NO:123) did not affect the activity of a closely related protease, aminopeptidase N (data not shown).
  • CPRECESIC (SEQ ID NO:123) inhibits migration and proliferation of endothelial cells.
  • CPRECESIC SEQ ID NO:123
  • CPRECESIC SEQ ID NO:123
  • CPRECESIC (SEQ ID NO:123) inhibits angiogenesis in vitro and in vivo
  • CPRECESIC SEQ ID NO:123
  • HUVECs plated on a three-dimensional matrix gel differentiate into a capillary-like structure, providing an in vitro model for angiogenesis.
  • Increasing concentrations of CPRECESIC (SEQ ID NO:123) peptide resulted in a progressive impairment of the formation of this network (not shown).
  • vessel-like branching structures were significantly fewer and shorter, and as a result, the cells could not form a complete network organization (not shown).
  • the control peptide GACVRLSACGA SEQ ID NO:124 did not affect HUVEC morphogenesis (not shown).
  • CAM chicken chorioallantoic membrane
  • An appropriate stimulus adsorbed on a gelatin sponge, induces microvessel recruitment to the sponge itself, accompanied by remodeling and ramification of the new capillaries.
  • Eight-day-old chicken egg CAMs were stimulated with VEGF-A alone (20 ng) or with VEGF-A plus CPRECESIC (SEQ ID NO:123) or GACVRLSACGA (SEQ ID NO:124) (1 mM) peptides. The CAMs were photographed at day 12.
  • Neovascularization induced by VEGF-A was inhibited by CPRECESIC (SEQ ID NO:123) by 40% based on the number of capillaries emerging from the sponge (Table 13).
  • the neovessels did not show the highly branching capillary structures typically seen after VEGF-A stimulation (not shown).
  • Treatment with control peptide GACVRLSACGA (SEQ ID NO:124) or with lower peptide concentrations of CPRECESIC (SEQ ID NO:123) had no effect on the number of growing vessels (not shown). Table 13.
  • CAM assay for angiogenesis TREATMENT BLOOD VESSEL NUMBERS No VEGF-A 12.0 ⁇ 2.82 * VEGF-A 57.0 ⁇ 1.41 * VEGF-A + control 56.5 ⁇ 2.12 VEGF-A + CPRECESIC (SEQ ID NO:123) 5.5 ⁇ 1.41 * *p ⁇ 0.01 with the Student-Newman-Keuls test. The results are expressed as the mean and standard error from two independent experiments.
  • mice show impaired neovascularization
  • APA +/- and APA -/- null mice were examined in a model of hypoxic retinopathy in premature mice. Induction of retinal neovascularization by relative hypoxia was already present in APA +/- mice compared to wild type mice (not shown). Neovascularization was almost undetectable in APA null mice (not shown). Neovascularization was quantified by counting vitreous protruding neovascular nuclei from 20 sections of hypoxic eyes. Significant induction of retinal neovascularization (16.17 ⁇ 1.19 neovascular nuclei/eye section) was seen in the wild type mice on postnatal day 17 (P17) after 75% oxygen treatment from P7 to P12.
  • neovascular nuclei Decreased amounts of neovascular nuclei were seen in the retinas of APA +/- (10.76 ⁇ 1.03 neovascular nuclei/eye section) and APA null (4.25 ⁇ 0.45 neovascular nuclei/eye section) mice on P17 after exposure to 75% oxygen from P7 to P12.
  • APA In vivo, APA is overexpressed by activated microvessels, including those in tumors, but it is barely detectable in quiescent vasculature, making it a suitable target for vessel-directed tumor therapy.
  • the present example identified a novel targeting peptide ligand for APA, CPRECESIC (SEQ ID NO:123). Soluble CPRECESIC (SEQ ID NO:123) peptide inhibited APA enzyme activity with an IC 50 of 800 ⁇ M.
  • soluble CPRECESIC (SEQ ID NO:123) peptide inhibited VEGF-A-induced migration and proliferation of HUVECs. These data are consistent with a requirement for migration and proliferation of endothelial cells during angiogenesis. CPRECESIC (SEQ ID NO:123) also blocked the formation of capillary-like structures in a Matrigel model and inhibited angiogenesis in VEGF-A-stimulated CAMs.
  • APA was shown to be important player in neovascularization induced by relative hypoxia, since APA null mice had significatively less retinal neovascularization compared to wt mice. These results strengthen the potential of using APA as a specific target for the inhibition of tumor angiogenesis.
  • the soluble peptide CPRECESIC (SEQ ID NO:123) is a selective APA ligand and inhibitor.
  • the inhibition of APA by CPRECESIC led to the inhibition of angiogenesis in different in vitro and in vivo assays, demonstrating for the first time a prominent role for APA in the angiogenic process.
  • APA-binding phage can home to tumor blood vessels, suggesting possible therapeutic uses of CPRECESIC (SEQ ID NO:123) as an inhibitor of tumor neovascularization.
  • the endogenous analog of CPRECESIC (SEQ ID NO:123) may be identified by antibody based purification or identification methods, similar to those disclosed above.
  • One method to accomplish such selective sampling is by PALM (Positioning and Ablation with Laser Microbeams).
  • the PALM Robot-MicroBeam uses a precise, computer-guided laser for microablation.
  • a pulsed ultra-violet (UV) laser is interfaced into a microscope and focused through an objective to a beam spot size of less than 1 micrometer in diameter.
  • the principle of laser cutting is a locally restricted ablative photodecomposition process without heating (Hendrix, 1999).
  • the effective laser energy is concentrated on the minute focal spot only and most biological objects are transparent for the applied laser wavelength. This system appears to be the tool of choice for recovery of homogeneous cell populations or even single cells or subcellular structures for subsequent phage recovery.
  • Tissue samples may be retrieved by circumcising a selected zone or a single cell after phage administration to the subject.
  • a clear-cut gap between selected and non-selected area is typically obtained.
  • the isolated tissue specimen can be ejected from the object plane and catapulted directly into the cap of a common microfuge tube in an entirely non-contact manner.
  • the basics of this so called Laser Pressure Catapulting (LPC) method is believed to be the laser pressure force that develops under the specimen, caused by the extremely high photon density of the precisely focused laser microbeam. This tissue harvesting technique allows the phage to survive the microdissection procedure and be rescued.
  • PALM was used in the present example to select targeting phage for mouse pancreatic tissue, as described below.
  • a CX 7 C peptide phage library (10 9 TU) was injected into the tail vein of a C57BL/6 male mouse, and the pancreas was harvested to recover the phage by bacterial infection. Phage from 246 colonies were grown separately in 5 mls LB/kanamycin (100 ⁇ g/ml)/tetracycline (40 ⁇ g/ml) at 37°C in the dark with agitation. Overnight cultures were pooled and the phage purified by NaCl/PEG precipitation for another round of in vivo bio-panning. Three hundred colonies were picked from the second round of panning, and the phage were recovered by precipitation. Phage from the second bio-panning round was then used for another round of in vivo panning and also was incubated with thawed frozen murine pancreatic sections for one in situ panning round.
  • Phage were recovered from cryo-preserved FITC-lectin stained mouse pancreatic islets and surrounding acinar cells that were microdissected from 14 ⁇ m sections using the PALM ( P ositioning and A blation with L aser M icrobeams) cold laser pressure catapulting system. Pancreatic islet and control sections were catapulted into 1 mM EDTA, pH 8, and frozen at -20 °C until enough material was collected for PCR amplification.
  • PALM P ositioning and A blation with L aser M icrobeams
  • Phage DNA was amplified with fUSE5 primers: forward primer 5' TAA TAC GAC TCA CTA TAG GGC AAG CTG ATA AAC CGA TAC AATT 3' (SEQ ID NO:132), reverse primer 5' CCC TCA TAG TTA GCG TAA CGA TCT 3' (SEQ ID NO:133).
  • the PCR products were subjected to another round of PCR using a nested set of primers. The 3' end of the second primer set was tailed with the M13 reverse primer for sequencing purposes.
  • the nested primer set used was: forward nested primer 5' CCTTTCTATTCTCACTCGGCCG 3' (SEQ ID NO:134), reverse nested primer 5' CAGGAAACAGCTATGACCGCTAAACAACTTTCAACAGTTTCGGC 3' (SEQ ID NO:135).
  • forward library primer 5' CACTCGGCCGACGGGGC 3' SEQ ID NO:136
  • reverse primer 5' CAGTTTCGGCCCCAGCGGCCC 3' SEQ ID NO:137.
  • PCR products generated from the nested primers were gel purified (Qiagen), and confirmed for the presence of a CX 7 C peptide insert sequence using the M13 reverse primer by automated sequencing.
  • PCR products generated from the library primers were gel purified (Qiagen), ligated into CsCl 2 purified fUSE5/SfiI, electroporated into electrocompetent MC1061 cells, and plated onto LB/streptomycin (100 ⁇ m/ml)/tetracycline (40 ⁇ g/ml) agar plates. Single colonies were subjected to colony PCR using the fUSE5 primers to verify the presence of a CX 7 C insert sequence by gel electrophoresis. Positive clones were sequenced using BigDye terminators (Perkin Elmer)
  • Pancreatic islet and control sections were catapulted into 1 mM AEBSF, 20 ⁇ g/ml aprotinin, 10 ⁇ g/ml leupeptin, 1 mM elastase inhibitor I, 0.1 mM TPCK, 1 nM pepstatin A in PBS, pH 7.4, and frozen for 48 hours or less until enough material was collected.
  • Each culture was transferred to 1.2 mls LB/Kan/Tet (0.2 ⁇ g/ml) and incubated in the dark at RT for 40 minutes. The tetracycline concentration was increased to 40 ⁇ g/ml for each culture, and the cultures were incubated overnight at 37 °C with agitation. Each culture was plated out the following day onto LB/Kan/Tet agar plates and incubated for 14 hours at 37 °C in the dark. Positive clones were picked for colony PCR and automated sequencing.
  • Table 14 lists selected targeting sequences and consensus motifs identified by pancreatic screening.
  • Table 14 Pancreatic targeting peptides and motifs Motif Peptide Sequence GGL (SEQ ID NO:138) CVPGLGGLC (SEQ ID NO:139) CGGLDVRMC (SEQ ID NO:140) CDGGLDWVC (SEQ ID NO:141) LGG (SEQ ID NO:142) CVPGLGGLC (SEQ ID NO:139)) CTWLGGREC (SEQ ID NO:143) CSRWGLGGC (SEQ ID NO:144) CPPLGGSRC (SEQ ID NO:251) VRG (SEQ ID NO:145) CVGGVRGGC (SEQ ID NO:146) CVGNDVRGC (SEQ ID NO:147) CESRLVRGC (SEQ ID NO:148) CGGRPVRGC (SEQ ID NO:149) AGG (SEQ ID NO:150) CTPFIAGGC (SEQ ID NO:151) CREWMAGGC (SEQ ID NO:152) CAGGSLR
  • FIG. 27 shows a general protocol for recovery of phage insert sequences from PALM selected thin section materials.
  • phage may be recovered by direct infection of E. coli host bacteria, after protease digestion of the thin section sample.
  • phage inserts may be recovered by PCR amplification and cloned into new vector DNA, then electroporated or otherwise transformed into host bacteria for cloning.
  • Pancreatic sequences recovered by direct bacterial infection included CVPRRWDVC (SEQ ID NO:194), CQHTSGRGC (SEQ ID NO:195), CRARGWLLC (SEQ ID NO:196), CVSNPRWKC (SEQ ID NO:197), CGGVHALRC (SEQ ID NO:175), CFNRTWIGC (SEQ ID NO:198) and CSRGPAWGC (SEQ ID NO:199).
  • Pancreatic targeting sequences recovered by amplification of phage inserts and cloning into phage include CWSRGQGGC (SEQ ID NO:200), CHVLWSTRC (SEQ ID NO:201), CLGLLMAGC (SEQ ID NO:202), CMSSPGVAC (SEQ ID NO:203), CLASGMDAC (SEQ ID NO:204), CHDERTGRC (SEQ ID NO:205), CAHHALMEC (SEQ ID NO:206), CMQGAATSC (SEQ ID NO:207), CMQGARTSC (SEQ ID NO:208) and CVRDLLTGC (SEQ ID NO:209).
  • FIG. 28 through FIG. 31 show sequence homologies identified for selected pancreatic targeting sequences.
  • Several proteins known to be present in pancreatic tissues are identified. The results of this example show that the PALM method may be used for selecting cell types from tissue thin sections and recovering targeting phage sequences. The skilled artisan will realize that this method could be used with virtually any tissue to obtain targeting sequences directed to specific types of cells in heterologous organs or tissues.

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